A Comparative View on Sex Differentiation and Gametogenesis Genes in Lungfish and Coelacanths

A Comparative View on Sex Differentiation and Gametogenesis Genes in Lungfish and Coelacanths Gonadal sex differentiation and reproduction are the keys to the perpetuation of favorable gene combinations and positively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits shared with actinopterygians, which disappeared in the tetrapod lineage. Key words: sex differentiation, gametogenesis, ovary, testis, evolution, Protopterus annectens, Latimeria menadoensis. Introduction sex determination modes, which either have a genetic basis or Sexual dimorphism is one of the most pervasive and diverse depend on other factors, for example, temperature popula- features of animal morphology, physiology, and behavior. The tion density, and visual cues. This divergence matches the process of gonad development involves complex and finely great variety of the initial triggers at the top of the gene net- tuned mechanisms that regulate gametogenesis, molecular work that direct the development toward a male or female sex determination, and gonad differentiation. Despite the phenotype, as well as the diversity of downstream acting generality of the phenomenon itself, sex determination, and components that implement and translate the initial signal differentiation mechanisms largely vary across metazoan taxa, into the development and differentiation of either testis or as the result of repeated, independent lineage-specific evolu- ovary from the bipotential embryonal gonad anlage (Herpin tion, and quick modification of the underlying molecular et al. 2013). This situation is particularly evident in teleost pathways. Within vertebrates, mammals and birds share a fishes, the largest group of extant chordates, where closely common genetic sex determining mechanism, which also dis- related species often display notably different sex determina- plays a remarkable degree of conservation at the molecular tion mechanisms (Kikuchi and Hamaguchi 2013). Despite this level. Others animal groups are characterized by highly diverse puzzling variability among species, some common principles The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com 1430 Genome Biol. Evol. 10(6):1430–1444. doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE are emerging from the analysis of the growing informa- Materials and Methods tion available about metazoan gonad sex development Male and female P. annectens specimens were obtained from molecular networks, for example, the recurrent involve- a local fish importer. Two testis, three ovaries, and one brain ment of certain molecules and pathways as primary male and liver sample each from a male and a female specimen sex determinants. Interestingly, some of these common- were used for total RNA isolation and sequencing as described alities mark teleosts as clearly different from those of previously (Biscotti et al. 2016). other vertebrate classes and, in some instances, of all Pieces of the gonads used in the transcriptome analyzes other tetrapods. These peculiarities might even include were fixed in 4% formaldehyde solution for 24 h at 4 C. the presence or absence of genes that are critical for go- Subsequently, the tissues were dehydrated, embedded in par- nadsex formationand gametogenesisinother branches affin, and then serially sectioned at 5 mm thickness. The sec- of the vertebrate phylogenetic tree. The study of sex de- tions were counterstained with hematoxylin and eosin (HE). termination and differentiation mechanisms in basal sar- The sex and the gonadal maturation stage of the animals copterygians represents a key to unveil whether the used for the generation of transcriptomes were confirmed by unique features displayed by teleosts exemplify an ances- histological analysis (fig. 1). The male gonad of P. annectens tral situation or they correspond to teleost-specific special- was classified as anastomosing tubular testis type, where izations. Coelacanths and lungfishes represent the closest tubules do not terminate at the testis periphery (Parenti and extant relatives to the tetrapod lineage, even though the Grier 2004). This type is common in the more basal bony latter have been shown to be phylogenetically closer to fishes, for example, salmonids, cyprinids, and lepisosteids the tetrapod stem (Biscotti et al. 2016; Irisarri and Meyer (Uribe et al. 2014). Both male gonadal tissues were at the 2016). Moreover, the morphological similarity between prereproductive stage (Schulz et al. 2010), with the MG1 the extant sarcopterygian fish and their fossil ancestors containing only few spermatogonias surrounded by Sertoli make them of outstanding scientific interest, considering cells. In MG6, the formation of individual tubules and their that they may also retain, to some extent, components of lumina are observed, and the germinal epithelium contains the molecular machinery of the last common ancestor of higher amounts of spermatogonia. The oogenesis in lung- tetrapods and fish. Due to the unique phylogenetic posi- fishes is similar to the teleost (Chaves 1992; Lubzens et al. tion of lungfish, their molecular studies are pivotal in un- 2010), and all three female gonads presented previtellogenic derstanding the evolution of vertebrates and the changes and vitellogenic oocytes. No postovulatory follicles were that accompanied the water-to-land transition. However, observed. molecular studies in lungfish and coelacanths in particular Sequences corresponding to key sex development-related are severely hampered by the difficult availability and genes were obtained by tBLASTn sequence homology maintenance of specimens in laboratory conditions. searches performed against the P. annectens and Latimeria Taking into account the impossibility of performing func- menadoensis transcriptomes (Canapa et al. 2012; Pallavicini tional studies in these species, the analysis of the gene et al. 2013; Biscotti et al. 2016) and the genomes of L. cha- expression profiles of sex differentiation and gametogen- lumnae (Amemiya et al. 2013), D. rerio (Howe et al. 2013), esis genes are the first choice for obtaining insights about and O. latipes (Kasahara et al. 2007). The sequence of sex gonad determination and differentiation. differentiation and gametogenesis-related genes previously Due to the paucity of biological material available from characterized in other species were used as queries and sim- coelacanths, the only study published so far on this topic ilarity thresholds were set on a case-by-case basis. Based on reported the expression of a few genes in the testis of the expression pattern and the so far functional analyzes of Latimeria menadoensis (Forconi et al. 2013). Whole genome those genes, we classified them in male- or female-related studies in Dipnoi have been long hindered by the enormous genes. The retrieved transcript sequences were translated us- size and high repeat content of their genomes. However, the ing the Sequence Translation (https://www.ebi.ac.uk/Tools/st/), publication of a reference transcriptome for the West African permitting to identify UTRs and CDSs. The orthology of each lungfish, Protopterus annectens (Biscotti et al. 2016)helped to transcript was confirmed using NCBI BLAST (http://blast.ncbi. overcome this major obstacle, finally allowing RNA-Seq-based nlm.nih.gov/Blast.cgi). Each transcript was used as query gene expression studies in this species. against the database<all nonredundant GenBank CDS The aim of this study was to expand the knowledge on translationsþ PDBþ SwissProtþ PIRþ PRF> excluding envi- basal sarcopterygian sex differentiation and gametogenesis by ronmental samples from WGS projects. characterizing 51 genes related to this process and assessing Orthologous sequences used in the phylogenetic analyses their expression levels in gonads. We find that the intermedi- were retrieved from GenBank (http://www.ncbi.nlm.nih.gov/) ate phylogenetic placement of lungfish, between acanthop- or ENSEMBL (http://www.ensembl.org/index.html) (for acces- terygian fish and tetrapods, is matched by the patterns of sion numbers see supplementary table 1, Supplementary molecular evolution of the sex differentiation and gameto- Material online). Multiple alignments of the amino acid genesis gene network. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1431 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE FIG.1.—Morphology of the gonads of Protopterus annectens.(A) Testes (MG1) revealing spermatogonias (asterisks) surrounded by Sertoli cells (arrowheads). (B) Testes (MG6) with completely formed tubules and lumina (Lu), and germinal epithelium containing spermatogonia (asterisks) and Sertoli cells (arrowheads). (C–E) Ovarian tissue (FG 2, 3, 4) containing pre–vitellogenic (PVO) and vitellogenic oocytes (VO). sequences were obtained with ClustalW (http://www.ge- to 0.75 and 0.98, respectively. Data from zebrafish and me- nome.jp/tools/clustalw/) using default parameters. daka were retrieved from the PhyloFish project database Phylogenetic analyses were performed by Bayesian infer- (Pasquier et al. 2016), BioProject PRJNA255848 and ence using MrBayes (version 3.2) (Huelsenbeck et al. 2001). PRJNA255889. In medaka, the sequence of the fgf24 tran- Substitution models as defined by posterior probabilities, sta- script, encoded by a gene present in a poorly assembled ge- tionarity, generations, sampling, burnin, and specific tree nomic region, was retrieved from the de novo assembled building parameters and rooting details are specified in the transcriptome. Raw reads counts were then converted to figure legend description of each tree. TPM values according to the formula suggested by Wagner The x rate (nonsynonymous/synonymous mutations) was et al. (2012) (supplementary fig. 1, Supplementary Material obtained with KaKs_calculator (Zhang et al. 2006) according online). Considering that absolute TPM expression values, in to Goldman and Yang (1994) (supplementary table 2, absence of biological replicates, might be quite variable be- Supplementary Material online). Poorly aligned positions and tween individuals and are therefore inappropriate for inter- divergent regions of alignments were eliminated by Gblocks species comparisons, we assigned expression ranges with the (Castresana 2000; Talavera and Castresana 2007). following categories for each gene: absent< 10 The expression levels of the selected genes in the different TPM,þ between 10 and 200,þþ between 200 and tissues and species were determined as described by Biscotti 700,þþþ between 700 and 2,000,þþþþ over 2,000. et al. (2016). Briefly, to ensure comparability among species, a Real-time quantitative PCRs of five genes (amh, ctnnb1, set of conserved orthologous genes present in L. menadoen- dmrt1, fgf9,and rspo1, for primers sequences see supplemen- sis, P. annectens,and D. rerio was selected as a reference for tary table 3, Supplementary Material online) were carried out the calculation of Transcripts Per Million (TPM). RNA-seq data in order to validate the transcriptome data. Reverse transcrip- from lungfish (Biscotti et al. 2016) (male and female gonads, tion was done using RevertAid First Strand Synthesis kit brain, and liver), coelacanth (Pallavicini et al. 2013) (male go- (Fermentas) and random primers. The reactions were per- nad, liver, and skeletal muscle), zebrafish (brain, liver, muscle, formed with SYBR Green reagent and amplifications were male and female gonads), and medaka (male and female detected with a Mastercycler ep realplex (Eppendorf). All gonads) were mapped to the reference nucleotide sequences results are averages of three independent PCR reactions with the CLC Genomics Workbench v.9 (Qiagen, Hilden, from cDNA preparations of three females and two males. Germany), setting length and similarity fraction parameters Transcript levels of target genes were normalized against 1432 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE Table 1 Identified Genes in Lungfish and Coelacanth Growth Factors amh amhr2 fgf9 fgf16 fgf20 fgf24 gsdf rspo1 wnt4 ptch2 hhip dhh pdgfa pdgfb pdgfra pdgfrb sdf1 cxcr4 Steroidogenic Enzymes srd5a1 srd5a2 srd5a3 cyp11b cyp19a1 Transcription Factors dmrt1 dmrt3 dmrt6 foxl2 foxl3 sf1 dax1 sox3 sox5 sox8 sox9 sox10 wt1 gata4 lrpprc pax2 Meiosis Regulation Genes aldh1a1 aldh1a2 aldh1a3 cyp26a1 cyp26b1 cyp26c1 stra8 Follistatin and b Catenin fst ctnnb1 Steroid Hormone Receptor Genes ar esra esrb Underlined genes were not found in lungfish. the lungfish eukaryotic translation initiation factor 4 gamma 1 growth factor-b (TGF-b) superfamily, which causes regression (eif4g1)gene. of the Mu ¨ llerian ducts during testicular differentiation in mammals. The high expression values of amh observed in male gonads of several vertebrates have been linked to the Results and Discussion proliferation and differentiation of spermatogonia (Skaar et al. In this paper, the presence of 51 genes known to be involved 2011; Hu et al. 2015). amh is also expressed in females, where in gonad sex differentiation and gametogenesis development it is restricted to the granulosa cells of ovarian follicles (Piprek, in other vertebrates was assessed in the transcriptomes of the Pecio, Laskowska-Kaszub, Kubiak, et al. 2013). Amh mainly lungfish P. annectens. This analysis allowed the identification acts through the Amhr2 signaling system in the development of 44 transcripts (table 1), all showing a complete CDS (sup- of gonadal tissue. Orthologous genes have been identified in plementary table 4, Supplementary Material online). The five several teleosts (Klu ¨ ver et al. 2007; Li et al. 2015; Pfennig et al. genes used for validation of the transcriptome by qRT-PCR 2015), despite the absence of Mu ¨ llerian ducts in these organ- showed mRNA levels consistent with the transcriptome data isms. In addition, Amh or its type II receptor act as Y-linked of the respective genes (supplementary table 5, male sex determining genes in some teleost species (Hattori Supplementary Material online). For comparison’s sake we et al. 2013; Kikuchi and Hamaguchi 2013; Herpin and Schartl also studied the sarcopterygian fish Latimeria, identifying 17 2015). On the other hand, the Mu ¨ llerian duct develops in new genes (table 1 and supplementary table 6, female coelacanths and lungfish (Hildebrand and Goslow Supplementary Material online) in addition to those investi- 2001) and in a basal group of actinopterygian fishes, the gated in our previous work (Forconi et al. 2013). The expres- sturgeons (Wrobel 2003). In lungfish and in the teleosts, sion levels (absent, low, intermediate, high) of the identified amh is preferentially expressed in male gonads and a robust genes were compared between the two basal sarcopterygians expression of this gene could be also observed in the testis of andwiththe teleosts Danio rerio and Oryzias latipes to provide Latimeria (table 2). the basis for a better understanding of the gene regulatory Like coelacanth and most other fish, lungfish possess a network governing gametogenesis and sex differentiation bona fide ortholog of amhr2 (supplementary fig. 2, and their evolution. Supplementary Material online). Unexpectedly, this gene is missing in the zebrafish genome. This appears to be species-specific feature, as amhr2 orthologs are present in Growth Factors and Their Receptors other teleost genomes. In medaka, amhr2 is highly expressed Anti-Mu ¨ llerian hormone (Amh), also known as Mu¨llerian in testis (supplementary fig. 1, Supplementary Material on- duct-inhibitory substance, is a member of the transforming line), and mutation of this gene leads to overproliferation of Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1433 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE Table 2 Growth Factors and Receptors Generally Related to Male Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary amh þ þ N.R. þþþþ  þþ þ amhr2 þ þ N.R. Absent þþ þ gsdf þ þ N.R. þþþþ þ þþþþ þþ fgf9 þ  N.R. Absent Absent fgf16 þ  N.R. fgf20a Absent  N.R. fgf20b þ fgf24 Absent  N.R. þþþ sdf1a þþþþ þ þ N.R. þþþ  þ þ sdf1b þ  þþ þ cxcr4a þþþþ þ þþ N.R. þþþþ cxcr4b þþ þþ a a pdgfaa þ þ þ N.R. þ pdgfab þ pdgfra þ þ N.R. þþþ pdgfb þ þ N.R. þþ pdgfrb þþ  N.R. þþþ Approximately 3-fold higher in ovary than testis. the germ cells in both testis and ovary, showing an important gene was already present in the common ancestor of role of Amh signaling in germ cell proliferation in adult gonad Chondrichthyes and Osteichthyes. (Morinaga et al. 2007). This gene is expressed in the testis of The high expression of gsdf in P. annectens testis (table 2)is Latimeria, whereas in the lungfish its expression is only found in line with data previously observed in coelacanth (Forconi in female gonads (table 2). This finding supports the presence et al. 2013) confirming the important role of this gene for of female expression bias of amhr2 in lungfish, like in tetra- male gonad development also in basal sarcopterygians. pods (Fagerberg et al. 2014; Jansson et al. 2016), but not in Furthermore, this pattern is in accordance with the well- Latimeria,where amhr2 is exclusively expressed in testis, like in described dimorphic expression of this gene in other fish spe- teleost fish, where a reverse organ expression pattern has cies (Kaneko 2015). gsdf can even act as master sex deter- been observed (Lubieniecki et al. 2015). mining gene (Myosho et al. 2012; Zhu et al. 2016)or as a Gonadal Soma-Derived Factor (GSDF) is another member male sex initiator, being activated by Dmrt1/Dmy (Zhang et al. of the TGF-b superfamily. This gene is particularly interesting 2016). because of its crucial function in fish testis development In summary, our results point out that a gsdf gene with (Zhang et al. 2016). Prior to our identification of a homolo- testis-specific function was retained in the sarcopterygian gous sequence in Latimeria (Forconi et al. 2013), gsdf was ancestors of tetrapods, only to be lost during the transition hypothesized to be a teleost innovation. Here, we report a from water to land. transcript encoding for gsdf also in P. annectens,whose R-spondin1 (Rspo1) is a regulator of the WNT/b-catenin orthology assessment is strongly supported by phylogenetic signaling pathway. This gene has been characterized as a fe- inference (fig. 2A). Moreover, as a distinctive feature, Gsdfs male sexual regulator in mammals, as it suppresses the male lack a glycine residue in the CxGxC motif, different from Inha axis and maintains oocyte survival by positively regulating and Amh proteins which have this amino acid (fig. 2B). The WNT4 signaling. In tetrapods and several teleosts, rspo1 presence of glycine in this motif is essential for heterodimer shows a sexually dimorphic expression pattern with higher formation of glycoprotein hormones (Kinoshita et al. 2006). values in the female gonad (Zhou et al. 2016), suggesting The functional meaning of this amino acid change for Gsdf is that Rspo1/Wnt/b-catenin signaling is an ancient pathway unknown, due to the lack of information about the signaling of ovarian differentiation in vertebrates. We found a quite pathway of this gene. The identification of a gsdf sequence in high expression for rspo1 in lungfish testis (table 3), and P. annectens implies its subsequent loss in the tetrapod line- much lower levels in ovaries. In zebrafish, rspo1 is equally age. Moreover, the additional identification of a gsdf se- expressed in ovary and testis, while in medaka no expression quence in the cartilaginous fish C. milii evidences that this was detected. rspo1 is also expressed in the ovary and testis of 1434 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.2.—Gsdf phylogeny. (A) Phylogenetic tree of Gsdf, Amh, and Inha amino acid sequences. Bayesian inference: 2,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.007, burn-in set to 5,000, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. (B) Multiple alignment of Gsdf, Amh, and Inha amino acid sequences showing the CxGxC conserved motif and the lack of the glycine residue, which is diagnostic for Gsdf proteins. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1435 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE Table 3 Growth Factors and Receptors Generally Related to Female Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary dhh þþ N.R. þ  þþ ptch2  N.R. þ þ hhip þ N.R. þþ þ þ þ ctnnb1 þþþ þþþþ þþþ N.R. þþþþ þþþþ þþþ þþ fst þ N.R. þ þ a a wnt4a þ N.R. þ þ a a wnt4b þ þ þ rspo1 þþ þ þ N.R. þþ Approximately 2- to 3-fold higher in testis than ovary. other teleosts, suggesting that it might be involved in both of fgf9 in C. milii dates back the origin of this gene to the ovarian and testicular development and spermatogenesis (Wu common ancestor of Chondrichthyes and Osteichthyes, im- et al. 2016). In other vertebrates, RSPO1 is widely expressed plying its loss in the lineage of Actinopterygii. Neither fgf9 nor (Han et al. 2015) and its transcript has been also detected in the other members of the FGF9/16/20 subfamily are adult human testis (Parma et al. 2006). Our findings suggest expressed in testis of lungfish and coelacanth (table 2). In that theroleof rspo1 in lungfish male gonads is not con- lungfish, we verified the absence of fgf20 both at the tran- nected to the action of wnt4, asthisgene is poorly expressed scriptome level. Moreover, fgf9 is strongly expressed in lung- in lungfish and coelacanth, while both wnt4 co-orthologs are fish ovary (table 2). This may indicate that the important well expressed in the gonads of zebrafish. Medaka, on the function of fgf9 for testis development is an innovation ac- other hand, presents relatively low expression of wnt4b in quired after the transition from water to land. testis. To evaluate the possible involvement of another member ß-catenin (Ctnnb1) is the critical molecule that transmits of the FGF gene family as a functional homolog of the tetra- the activity of the female determining pathway signals of pod Fgf9, as recently proposed by Leerberg et al. (2017),we Wnt4 and R-spondin to the nucleus to activate effector genes. took a closer look at fgf24, a member of the FGF8/17/18/24 High expression values were recorded for ctnnb1 in all four family (fig. 4). The isolation of this gene in the elephant shark species (table 3). While no strong sex bias in expression is supported its presence in the common ancestor of gna- present in zebrafish and medaka, the lungfish ovary shows thostomes (Jovelin et al. 2010). Within the sarcopterygian considerably higher levels than testis, in contrast with the ex- lineage, fgf24 could be only identified in Latimeria pression pattern of wnt4 and rspo1 (table 3). (Amemiya et al. 2013) but not in tetrapods (Jovelin et al. Follistatin (Fst) encodes a TGFß superfamily binding protein 2010). In addition, no orthologous sequence to fgf24 that acts downstream of WNT4 to maintain germ cell survival could be retrieved from the P. annectens transcriptome, in the cortical domain of the mammalian ovary (Yao et al. which might either indicate the lack of expression of this 2004). This gene is present in both basal sarcopterygians. The gene, or its loss. If confirmed at the genome level, this lack expression of fst in lungfish, in line with the absence of finding might indicate that fgf24 was lost in the common detectable expression for wnt4 (table 3), may be connected to ancestor of lungfish and tetrapods. This gene is expressed the prereproductive stage of the female gonads. in the early somatic and in adult gonads of zebrafish Fibroblast Growth Factors (Fgf) are a family of small pro- Leerberg et al. (2017) (table 2) and was suggested as a teins that have multiple functions in regulating cellular devel- plausible candidate to substitute for fgf9 function in tele- opment and growth. Numerous studies in mice have shown osts. In addition, fgf24 is expressed only in testis of adult that FGF9 plays an important role in testis development, cre- medaka. ating a positive feedback loop with Sox9 and antagonizing Stromal-cell-derived factor 1 (Sdf1, also known as Cxcl12) Wnt4, an ovarian factor (Jameson et al. 2012). No orthologs is a chemokine involved in a wide variety of body functions. It of fgf9 have been identifiedinactinopterygian fishsofar (Itoh binds to CXC receptor 4 (Cxcr4), a G-coupled transmembrane and Konishi 2007). The identification of fgf9 in Latimeria has glycoprotein located on the surface membranes of primordial previously suggested that this gene was present in the com- germ cells. The interaction between Sdf1 and its receptor mon ancestor of Sarcopterygii (Forconi et al. 2013), a hypoth- regulates migration and proliferation of various cell types, esis which is now further supported by the retrieval of this which importantly comprise also teleosts primordial germ sequence also in P. annectens (fig. 3). Moreover, the presence cells. Previous studies assigned a central role to Sdf1 and 1436 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.3.—Fgf9/16/20 phylogeny. Phylogenetic analysis of Fgf9, Fgf16, Fgf20. Bayesian inference: 1,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.0055, burn-in set to 2,500, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. CXCR4 in the development of embryonic and postnatal go- Steroidogenic Enzymes nad (Yang et al. 2013; Westernstro ¨ er et al. 2014; Fernandez Steroid-5-Alpha-Reductase Alpha Polypeptides 1, 2, 3 et al. 2015). In human adults, the expression of SDF1 was (Srd5a1, Srd5a2, Srd5a3) are proteins involved in the conver- observed in Sertoli cells. The expression of Cxcr4 in adult sion of testosterone to dihydrotestosterone (DHT), a very po- mouse testis (Yang et al. 2013) further suggests a role for tent androgen in teleosts fishes and tetrapods. Unexpectedly, the ligand/receptor in spermatogenesis. Both genes are pref- we detected higher expression of srd5a1 in lungfish ovary, in erentially expressed in lungfish male gonads (table 2), at par- contrast to its absence in zebrafish and the low expression in ticularly high levels in the more immature testis sample. In female medaka (supplementary table 7, Supplementary addition, the expression of these genes has been also recently Material online). Srd5a1 is predominantly expressed in the reported in both male and female gonads of the teleost female gonads of frogs but also in rat (Lephart et al. 1992) Oreochromis mossambicus (Amat-Fernandez et al. 2017). and human (Haning et al. 1996; Mahendroo and Russell Platelet-derived growth factors (Pdgf) and their receptors 1999), consistently with our observations in lungfish (supple- are involved in regulating the development of various tissues mentary table 7, Supplementary Material online). This finding (Miura et al. 2002). In particular, they play a fundamental role suggests that Srd5a1 might confer the ability of metabolizing in the development of gonadal tissue in mammalian fetal and testosterone into DHT in the sarcopterygian lineage, while a adult testis (Li et al. 2016). In zebrafish and medaka, this gene different isozyme is likely used in teleost fish. is preferentially expressed in testis (table 2). However, in both Cytochrome P450 19A1 (Cyp19a1 or aromatase) cata- sarcopterygians, the expression of pdgfs and their receptors in lyzes the final step in the biosynthesis of estrogens, which testis were quite low. The lungfish pdgfa and pdgfrb ortho- have a key role in ovarian differentiation and maintenance logs unexpectedly showed the highest expression levels in in fish, amphibians, reptiles, and birds (Bruggeman et al. ovary (table 2). Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1437 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE FIG.4.—Fgf8/17/18/24 phylogeny. Phylogenetic analysis of Fgf8, Fgf17, Fgf18, Fgf24. Bayesian inference: 2,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.0062, burn-in set to 5,000, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. 2002; Dumond et al. 2008; Lubieniecki et al. 2015). The detect 11-ketotestosterone in Australian lungfish (Joss et al. expression patterns observed in the present study is con- 1996). sistent with a conserved function for this gene also in basal sarcopterygians (supplementary table 8, Steroid Hormone Receptors Supplementary Material online). Cytochrome P450 11c1 (Cyp11c1). In most teleost fish the The expression of steroidogenic enzymes is usually connected predominant androgen is 11-ketotestosterone, which is pro- to the production of biologically active estrogens and andro- duced from testosterone by the action of the cyp11c1 gene. gens. The action of these steroid hormones requires the pres- However, tetrapod cyp11B homologs function predominantly ence of the cognate receptors, whose transcription is often in adrenal steroid biosynthesis and are not expressed in testis further up-regulated by the presence of hormones in a posi- (Schiffer et al. 2015). A gene pertaining to the CYP11 sub- tive feedback loop. We found a very unexpected expression family is present in lungfish as well as in the coelacanth (sup- pattern for these receptors in lungfish. Indeed, while the an- plementary fig. 3, Supplementary Material online). The drogen receptor (ar) was expressed in the mature testis of absence of expression in the gonads of these two species is coelacanth and teleost, no expression could be detected in in line with the results of a previous study, which failed to lungfish male gonad nor in any other tissue (supplementary 1438 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE Table 4 Transcription Factors Generally Related to Male Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary dmrt1 þþ þ þþ N.R. þþþþ þ þþ þ dmrt3  N.R. þ þ dmrt6 þþ þ þþþ N.R. Absent Absent sox3  N.R. þ þ sox5 þ N.R. þþþ   þ sox8a þ N.R. þþþ sox8b þþþþ þ a a sox9a þ þ þþ N.R. þ þ þ b b sox9b þ þ þ sox10 þ N.R. þ gata4 þþ N.R. þ þ þ lrpprc þþ þþþ þþ N.R. þþþ þþþ þ þþ sf1 þþþ þ þ N.R. þþþþ þþþþ þþ þ wt1a þþ N.R. þþ þ þ þ wt1b þþ pax2a þ N.R. þ pax2b þ In ovary barley above background, but robust expression in testis. Approximately 3-fold higher in ovary than testis. table 7, Supplementary Material online). Whether this ab- Although no dmrt6 gene has been annotated yet in any of the sence is linked to the nonreproductive stage of the gonads fully sequenced teleost genomes, a recent publication or to the use of another nuclear receptor for sensing andro- reported dmrt6-like sequences in spotted gar, cichlids, and gen levels in lungfish remains an interesting question to be siluriforms. This dmrt6-like gene was expressed in spermato- approached in the future. Teleost esrs were also preferentially cytes and its function was shown to be involved in spermato- expressedintestis(supplementary table 8, Supplementary genesis in tilapia (Zhang, Wang, et al. 2014). The loss of this Material online). On the other hand, mammalian ESRsare gene in some teleost lineages could represent another aspect produced at very low levels in testis (Cavaco et al. 2009). of the extreme variability of the genetic network involved in The exceptionally high levels identified in lungfish male sex determination and differentiation in fish. Overall, the pres- gonads may be related to the premature status of the tissues ence and expression of dmrt6 in basal sarcopterygians sup- available for this study (supplementary table 7, Supplementary ports an ancient and conserved function for this gene in testis Material online). development and function. The Steroidogenic Factor 1 (Sf1) was mainly expressed in lungfish and coelacanth testis, while in zebrafish it showed a Transcription Factors broader tissue distribution (table 4). Sf1 is expressed in both sexes in mice fetal gonads, but in later developmental stages it Doublesex- and mab-3-related transcriptional factor 1 continues to be expressed only in testes, where it is activated (Dmrt1), together with Amh and Sox9, is important for ver- and maintained by Wilms tumor 1 (WT1). On the other hand, tebrate testicular differentiation. Its expression of dmrt1 in Sf1 is down-regulated by Forkhead box L2 (FOXL2) in ovary lungfish (table 4) is in agreement with the dimorphic expres- (Takasawa et al. 2014). The low expression of sf1 observed in sion pattern observed from fish to mammals (Websteretal. lungfish ovary, opposed to the high expression detected in 2017) and suggest a major role in adult testis function. zebrafish female gonad, is in line with the mammalian In contrast to other vertebrates (Bratus and Słota 2009), no pattern. trace of dmrt3 expression was detected in the two basal sar- SRY-related HMG box (SOX) family proteins are transcrip- copterygians (table 4). On the other hand, the expression of tion factors involved in many developmental processes. In dmrt6 in lungfish and coelacanth testis is intriguing (table 4). particular, sox3, sox5, sox8, sox9,and sox10 have a function In mice, this gene is likely involved in directing the transition in gonad development. SOX3 belongs to subfamily B and from spermatogonia to spermatocytes (Zhang, Murphy, et al. is the ancestor of SRY (Marshall-Graves 2008). Although 2014). This study allows to extend the taxonomic range dis- sox3 is not required for sex determination in mammals tribution of dmrt6 from tetrapods to basal sarcopterygians. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1439 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE (Weiss et al. 2003), it is the master male sex determining gene in the fish Oryzias dancena (Takehana 2014). sox5, pertaining to the subfamily D, is a regulator of male germ cells in medaka (Schartl et al. 2018). It is expressed in mice postnatal testis and, together with Sox9 and Sox13, it may play a role in spermatogenesis (Daigle et al. 2015). The other three genes belong to subfamily E: SOX9 is activated by SRY in mammals and is required for sex determination in tetrapods (Jakob and Lovell-Badge 2011); whereas Sox8 is activated by SOX9 and acts in a positive feedback loop on Sox9 in testis differentia- tion, as shown in mice. All five sox genes are present in the lungfish transcriptome. In Latimeria, in addition to the sox8/9/ 10 sequences identified in our previous work (Forconi et al. 2013), we can report the identification of sox3 (from the ge- nome) and sox5 (from transcriptome data). The orthology status of the isolated sequences was assessed by phylogenetic analysis (supplementary fig. 4, Supplementary Material online) FIG.5.—Stra8 phylogeny. Phylogenetic analysis of Stra8. Bayesian that assigned each sequence to the corresponding sox gene inference: 1,000,000 generations, sampling every 100, Jones substitution clade. model, stationarity defined as when the average SD of split frequencies The tissue distribution of sox3 transcripts confirms that the approaching 0.0033, burn-in set to 2,500, midpoint rooting. Numbers almost exclusive role of this gene in brain is also retained in close to nodes indicate posterior probability values. Only values >95 basal sarcopterygians (table 4). Together with SOX1 and were reported. The sequences in bold were obtained in this work. SOX2, the other two paralogs of the B1 group of the SOX family, SOX3 plays a key role in central nervous system devel- coelacanth, lungfish, and zebrafish. Expression of foxl3 in opment in mouse (Rogers et al. 2013). sox8 was neither the gonad was observed only in medaka, indicating a diver- expressed in Latimeria (Forconi et al. 2013) nor in lungfish gent role of this gene between different vertebrates. This testis (table 4). In mammals, the action of SOX8 in the gene has not been identified in placental mammals and in FGF9/SOX9 interaction loop is important for testis mainte- amphibians (Bertho et al. 2016) and, except from the study in nance (Barrionuevo et al. 2009). The lack of expression of medaka, its gonadal function remains unclear. both sox8 and fgf9 hints that this interaction loop, which is crucial in mammalian sex determination, is not yet in place in Meiosis Regulation Genes basal sarcopterygians. Both sox9 and wt1 are expressed in lungfish and coelacanth testis, in line with their known pat- Meiosis is one of the most important processes in sexual re- tern of distribution in tetrapods. production, as it produces haploid gametes. However, regu- Forkhead transcription factors (Fox) are involved in many lation of the meiotic program is still insufficiently understood biological processes, including the regulation of cell prolifera- in most species. In mammals, the morphogen retinoic acid tion and differentiation, tissue development, and various met- triggers meiotic entry through up-regulation of the abolic processes. Foxl2 plays a key role in the early Stimulated by retinoic acid gene 8 (Stra8). This gene encodes development of vertebrate female gonads and, in adults, a retinoic acid-responsive protein that plays a critical role in has an ovarian function. In particular FOXL2 suppresses the regulation of meiotic initiation during spermatogenesis Dmrt1 for maintaining female fate (Matson et al. 2011) and oogenesis (Feng et al. 2014). Commonly present in tetra- and, together with WNT4, cooperates in regulating Fst ex- pods, this gene is absent in some teleosts species, including pression during ovarian development (Garcia-Ortiz et al. zebrafish (Rodrıguez-Marı et al. 2013). A more comprehen- 2009). It regulates estrogen synthesis via up-regulation of sive analysis of the evolution of stra8 suggests that this gene Cyp19A1a (Pannetier et al. 2006). In medaka, the paralogous was lost in Acanthomorpha and, independently, in the gene foxl3 encodes a protein that may play a role in sexual Cypriniform lineage within Actinopterygii (Pasquier et al. fate decision in germ cells by suppressing spermatogenesis 2016). We can however report the presence of this gene in (Nishimura et al. 2015). While both these genes are present the two basal sarcopterygian species. Phylogenetic analysis in the genome of L. chalumnae, only foxl2 was found in the P. positioned the lungfish and coelacanth sequences at a basal annectens transcriptome. The sequences identified were used position compared with tetrapods (fig. 5). for phylogenic analyzes (supplementary fig. 5, Supplementary The level of the retinoic acid as a meiosis signal is deter- Material online). foxl2 was expressed in lungfish female mined by the antagonistic action of enzymes involved in its gonads (supplementary table 9, Supplementary Material on- synthesis and degradation: the enzyme ALDH1a2, a member line). No expression of foxl3 was however detected in of the retinaldehyde dehydrogenase family, is responsible for 1440 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.6.—Summarizing scheme of sex-related genes lost in the main vertebrate lineages. The scheme shows the sex genes lost in tetrapods, lungfish, coelacanth, and teleosts. The colours are referred to the functional groups, respectively. its synthesis, while CYP26B1 encodes a major retinoic acid- (supplementary table 2, Supplementary Material online). All degrading enzyme. In mice, down-regulation of Cyp26b1 in genes appear to evolve under purifying selection (Ka/Ks<1) femalesleadstohighlevels of retinoic acid, whichin turn with the exception of the x rate obtained between the two induce the expression of the premeiotic marker Stra8, thereby gsdf co-orthologs in D. rerio. allowing female germ cells to enter meiosis. Cyp26b1 acts as a Our analysis of lungfish ovary and testis transcriptomes and meiosis-inhibiting factor in mammals, birds, and amphibians the comparison with similar data sets from both zebrafish and (Bowles and Koopman 2010; Piprek, Pecio, Laskowska- medaka, and with the testis transcriptome of coelacanth Kaszub, Kloc, et al. 2013; Yu et al. 2013), while in teleosts revealed a situation that reflects the peculiar phylogenetic this role is exerted by cyp26a1 (Adolfi et al. 2016). position of the Dipnoi. We identified some genes whose ex- We found high expression of cyp26b1 and stra8 in pression pattern in lungfish and, as far as testis is concerned, lungfish and coelacanth male gonads suggesting that also in Latimeria is more similar to teleosts than tetrapods. As basal sarcopterygians follow the tetrapod pattern (sup- an example, gsdf, which is an important male determining plementary table 10, Supplementary Material online). gene in teleosts, but which is missing in the tetrapod lineage, However, significant differences were observed in the was present and highly expressed in testis of both lungfish expression of aldh1as: aldh1a1 showed higher expres- and coelacanth. sion in lungfish male gonads, and is therefore the only On the other hand, a number of other genes present in gene responsible for retinoic acid synthesis in coelacanth lungfish display a behavior more similar to tetrapods than testis (supplementary table 10, Supplementary Material teleost fishes, for example, srd5a1, which was highly online). Such lineage specific subfunctionalization of ret- expressed in lungfish ovary, like in tetrapods, or b-catenin, inoic acid metabolizing enzymes has also been reported the transcription factor readout of the female gonad spe- in a comparative study among different teleost fish cific tetrapod signaling cascade, which was also highly (Canestro et al. 2009). cyp26c1 was not found in the expressed in lungfish ovary. Intriguingly, the upstream ef- lungfish transcriptome, marking a possible lineage- fector R-spondin1 does not follow this pattern. At the specific loss. same time wnt4, which is an ovary specific gene in tetra- pods and an upstream regulator of ß-catenin, is highly expressed in teleost testis and did not show significant Conclusions expression in lungfish and coelacanth gonad samples. Our analysis of sex differentiation and gametogenesis genes Sf1 is a male specific gene in mammals and lungfish go- in lungfish and coelacanth revealed a complex picture. None nad, which was also highly expressed in Latimeria testis. of the gene-encoded protein products showed any unusual stra8 is absent from many major teleost lineages, but it is structural feature, like missing or additional domains or unex- present and highly expressed in the testis of basal sarcop- pectedly high sequence divergence. We calculated the x rates terygians, following the tetrapod profile. Dmrt6, a gene for genes that were of special interest due to their appear- which has an important function in mammalian spermato- ance/disappearance at the split of sarcopterygians and actino- genesis and which is only seldom found in teleost pterygians (fgf9, foxl3, gsdf,and stra8), in lungfish, genomes, showed high expression in lungfish and coela- coelacanth and other representative vertebrates canth testis, indicating functional conservation. The Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1441 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE reasons underpinning the possible loss of such an impor- the conception of the study and the experimental design and tant gene in most teleosts—similar but independent from have given final approval for the version to be published. stra8—are totally unclear. Finally, some lungfish and coelacanth genes follow nei- Literature Cited ther the teleost nor the tetrapod scheme. Fgf9 is an im- Adolfi MC, Herpin A, Regensburger M, Sacquegno J, Waxman JS. 2016. portant male sex determining gene in tetrapods, which is Retinoic acid and meiosis induction in adult versus embryonic gonads absent in teleosts. Our analysis demonstrates that fgf9 has of medaka. Sci Rep. 6:34281. been specifically lost in the teleost lineage and the ab- Amat-Fernandez J, et al. 2017. 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Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Genome Biology and Evolution Oxford University Press

A Comparative View on Sex Differentiation and Gametogenesis Genes in Lungfish and Coelacanths

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Abstract

Gonadal sex differentiation and reproduction are the keys to the perpetuation of favorable gene combinations and positively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits shared with actinopterygians, which disappeared in the tetrapod lineage. Key words: sex differentiation, gametogenesis, ovary, testis, evolution, Protopterus annectens, Latimeria menadoensis. Introduction sex determination modes, which either have a genetic basis or Sexual dimorphism is one of the most pervasive and diverse depend on other factors, for example, temperature popula- features of animal morphology, physiology, and behavior. The tion density, and visual cues. This divergence matches the process of gonad development involves complex and finely great variety of the initial triggers at the top of the gene net- tuned mechanisms that regulate gametogenesis, molecular work that direct the development toward a male or female sex determination, and gonad differentiation. Despite the phenotype, as well as the diversity of downstream acting generality of the phenomenon itself, sex determination, and components that implement and translate the initial signal differentiation mechanisms largely vary across metazoan taxa, into the development and differentiation of either testis or as the result of repeated, independent lineage-specific evolu- ovary from the bipotential embryonal gonad anlage (Herpin tion, and quick modification of the underlying molecular et al. 2013). This situation is particularly evident in teleost pathways. Within vertebrates, mammals and birds share a fishes, the largest group of extant chordates, where closely common genetic sex determining mechanism, which also dis- related species often display notably different sex determina- plays a remarkable degree of conservation at the molecular tion mechanisms (Kikuchi and Hamaguchi 2013). Despite this level. Others animal groups are characterized by highly diverse puzzling variability among species, some common principles The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com 1430 Genome Biol. Evol. 10(6):1430–1444. doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE are emerging from the analysis of the growing informa- Materials and Methods tion available about metazoan gonad sex development Male and female P. annectens specimens were obtained from molecular networks, for example, the recurrent involve- a local fish importer. Two testis, three ovaries, and one brain ment of certain molecules and pathways as primary male and liver sample each from a male and a female specimen sex determinants. Interestingly, some of these common- were used for total RNA isolation and sequencing as described alities mark teleosts as clearly different from those of previously (Biscotti et al. 2016). other vertebrate classes and, in some instances, of all Pieces of the gonads used in the transcriptome analyzes other tetrapods. These peculiarities might even include were fixed in 4% formaldehyde solution for 24 h at 4 C. the presence or absence of genes that are critical for go- Subsequently, the tissues were dehydrated, embedded in par- nadsex formationand gametogenesisinother branches affin, and then serially sectioned at 5 mm thickness. The sec- of the vertebrate phylogenetic tree. The study of sex de- tions were counterstained with hematoxylin and eosin (HE). termination and differentiation mechanisms in basal sar- The sex and the gonadal maturation stage of the animals copterygians represents a key to unveil whether the used for the generation of transcriptomes were confirmed by unique features displayed by teleosts exemplify an ances- histological analysis (fig. 1). The male gonad of P. annectens tral situation or they correspond to teleost-specific special- was classified as anastomosing tubular testis type, where izations. Coelacanths and lungfishes represent the closest tubules do not terminate at the testis periphery (Parenti and extant relatives to the tetrapod lineage, even though the Grier 2004). This type is common in the more basal bony latter have been shown to be phylogenetically closer to fishes, for example, salmonids, cyprinids, and lepisosteids the tetrapod stem (Biscotti et al. 2016; Irisarri and Meyer (Uribe et al. 2014). Both male gonadal tissues were at the 2016). Moreover, the morphological similarity between prereproductive stage (Schulz et al. 2010), with the MG1 the extant sarcopterygian fish and their fossil ancestors containing only few spermatogonias surrounded by Sertoli make them of outstanding scientific interest, considering cells. In MG6, the formation of individual tubules and their that they may also retain, to some extent, components of lumina are observed, and the germinal epithelium contains the molecular machinery of the last common ancestor of higher amounts of spermatogonia. The oogenesis in lung- tetrapods and fish. Due to the unique phylogenetic posi- fishes is similar to the teleost (Chaves 1992; Lubzens et al. tion of lungfish, their molecular studies are pivotal in un- 2010), and all three female gonads presented previtellogenic derstanding the evolution of vertebrates and the changes and vitellogenic oocytes. No postovulatory follicles were that accompanied the water-to-land transition. However, observed. molecular studies in lungfish and coelacanths in particular Sequences corresponding to key sex development-related are severely hampered by the difficult availability and genes were obtained by tBLASTn sequence homology maintenance of specimens in laboratory conditions. searches performed against the P. annectens and Latimeria Taking into account the impossibility of performing func- menadoensis transcriptomes (Canapa et al. 2012; Pallavicini tional studies in these species, the analysis of the gene et al. 2013; Biscotti et al. 2016) and the genomes of L. cha- expression profiles of sex differentiation and gametogen- lumnae (Amemiya et al. 2013), D. rerio (Howe et al. 2013), esis genes are the first choice for obtaining insights about and O. latipes (Kasahara et al. 2007). The sequence of sex gonad determination and differentiation. differentiation and gametogenesis-related genes previously Due to the paucity of biological material available from characterized in other species were used as queries and sim- coelacanths, the only study published so far on this topic ilarity thresholds were set on a case-by-case basis. Based on reported the expression of a few genes in the testis of the expression pattern and the so far functional analyzes of Latimeria menadoensis (Forconi et al. 2013). Whole genome those genes, we classified them in male- or female-related studies in Dipnoi have been long hindered by the enormous genes. The retrieved transcript sequences were translated us- size and high repeat content of their genomes. However, the ing the Sequence Translation (https://www.ebi.ac.uk/Tools/st/), publication of a reference transcriptome for the West African permitting to identify UTRs and CDSs. The orthology of each lungfish, Protopterus annectens (Biscotti et al. 2016)helped to transcript was confirmed using NCBI BLAST (http://blast.ncbi. overcome this major obstacle, finally allowing RNA-Seq-based nlm.nih.gov/Blast.cgi). Each transcript was used as query gene expression studies in this species. against the database<all nonredundant GenBank CDS The aim of this study was to expand the knowledge on translationsþ PDBþ SwissProtþ PIRþ PRF> excluding envi- basal sarcopterygian sex differentiation and gametogenesis by ronmental samples from WGS projects. characterizing 51 genes related to this process and assessing Orthologous sequences used in the phylogenetic analyses their expression levels in gonads. We find that the intermedi- were retrieved from GenBank (http://www.ncbi.nlm.nih.gov/) ate phylogenetic placement of lungfish, between acanthop- or ENSEMBL (http://www.ensembl.org/index.html) (for acces- terygian fish and tetrapods, is matched by the patterns of sion numbers see supplementary table 1, Supplementary molecular evolution of the sex differentiation and gameto- Material online). Multiple alignments of the amino acid genesis gene network. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1431 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE FIG.1.—Morphology of the gonads of Protopterus annectens.(A) Testes (MG1) revealing spermatogonias (asterisks) surrounded by Sertoli cells (arrowheads). (B) Testes (MG6) with completely formed tubules and lumina (Lu), and germinal epithelium containing spermatogonia (asterisks) and Sertoli cells (arrowheads). (C–E) Ovarian tissue (FG 2, 3, 4) containing pre–vitellogenic (PVO) and vitellogenic oocytes (VO). sequences were obtained with ClustalW (http://www.ge- to 0.75 and 0.98, respectively. Data from zebrafish and me- nome.jp/tools/clustalw/) using default parameters. daka were retrieved from the PhyloFish project database Phylogenetic analyses were performed by Bayesian infer- (Pasquier et al. 2016), BioProject PRJNA255848 and ence using MrBayes (version 3.2) (Huelsenbeck et al. 2001). PRJNA255889. In medaka, the sequence of the fgf24 tran- Substitution models as defined by posterior probabilities, sta- script, encoded by a gene present in a poorly assembled ge- tionarity, generations, sampling, burnin, and specific tree nomic region, was retrieved from the de novo assembled building parameters and rooting details are specified in the transcriptome. Raw reads counts were then converted to figure legend description of each tree. TPM values according to the formula suggested by Wagner The x rate (nonsynonymous/synonymous mutations) was et al. (2012) (supplementary fig. 1, Supplementary Material obtained with KaKs_calculator (Zhang et al. 2006) according online). Considering that absolute TPM expression values, in to Goldman and Yang (1994) (supplementary table 2, absence of biological replicates, might be quite variable be- Supplementary Material online). Poorly aligned positions and tween individuals and are therefore inappropriate for inter- divergent regions of alignments were eliminated by Gblocks species comparisons, we assigned expression ranges with the (Castresana 2000; Talavera and Castresana 2007). following categories for each gene: absent< 10 The expression levels of the selected genes in the different TPM,þ between 10 and 200,þþ between 200 and tissues and species were determined as described by Biscotti 700,þþþ between 700 and 2,000,þþþþ over 2,000. et al. (2016). Briefly, to ensure comparability among species, a Real-time quantitative PCRs of five genes (amh, ctnnb1, set of conserved orthologous genes present in L. menadoen- dmrt1, fgf9,and rspo1, for primers sequences see supplemen- sis, P. annectens,and D. rerio was selected as a reference for tary table 3, Supplementary Material online) were carried out the calculation of Transcripts Per Million (TPM). RNA-seq data in order to validate the transcriptome data. Reverse transcrip- from lungfish (Biscotti et al. 2016) (male and female gonads, tion was done using RevertAid First Strand Synthesis kit brain, and liver), coelacanth (Pallavicini et al. 2013) (male go- (Fermentas) and random primers. The reactions were per- nad, liver, and skeletal muscle), zebrafish (brain, liver, muscle, formed with SYBR Green reagent and amplifications were male and female gonads), and medaka (male and female detected with a Mastercycler ep realplex (Eppendorf). All gonads) were mapped to the reference nucleotide sequences results are averages of three independent PCR reactions with the CLC Genomics Workbench v.9 (Qiagen, Hilden, from cDNA preparations of three females and two males. Germany), setting length and similarity fraction parameters Transcript levels of target genes were normalized against 1432 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE Table 1 Identified Genes in Lungfish and Coelacanth Growth Factors amh amhr2 fgf9 fgf16 fgf20 fgf24 gsdf rspo1 wnt4 ptch2 hhip dhh pdgfa pdgfb pdgfra pdgfrb sdf1 cxcr4 Steroidogenic Enzymes srd5a1 srd5a2 srd5a3 cyp11b cyp19a1 Transcription Factors dmrt1 dmrt3 dmrt6 foxl2 foxl3 sf1 dax1 sox3 sox5 sox8 sox9 sox10 wt1 gata4 lrpprc pax2 Meiosis Regulation Genes aldh1a1 aldh1a2 aldh1a3 cyp26a1 cyp26b1 cyp26c1 stra8 Follistatin and b Catenin fst ctnnb1 Steroid Hormone Receptor Genes ar esra esrb Underlined genes were not found in lungfish. the lungfish eukaryotic translation initiation factor 4 gamma 1 growth factor-b (TGF-b) superfamily, which causes regression (eif4g1)gene. of the Mu ¨ llerian ducts during testicular differentiation in mammals. The high expression values of amh observed in male gonads of several vertebrates have been linked to the Results and Discussion proliferation and differentiation of spermatogonia (Skaar et al. In this paper, the presence of 51 genes known to be involved 2011; Hu et al. 2015). amh is also expressed in females, where in gonad sex differentiation and gametogenesis development it is restricted to the granulosa cells of ovarian follicles (Piprek, in other vertebrates was assessed in the transcriptomes of the Pecio, Laskowska-Kaszub, Kubiak, et al. 2013). Amh mainly lungfish P. annectens. This analysis allowed the identification acts through the Amhr2 signaling system in the development of 44 transcripts (table 1), all showing a complete CDS (sup- of gonadal tissue. Orthologous genes have been identified in plementary table 4, Supplementary Material online). The five several teleosts (Klu ¨ ver et al. 2007; Li et al. 2015; Pfennig et al. genes used for validation of the transcriptome by qRT-PCR 2015), despite the absence of Mu ¨ llerian ducts in these organ- showed mRNA levels consistent with the transcriptome data isms. In addition, Amh or its type II receptor act as Y-linked of the respective genes (supplementary table 5, male sex determining genes in some teleost species (Hattori Supplementary Material online). For comparison’s sake we et al. 2013; Kikuchi and Hamaguchi 2013; Herpin and Schartl also studied the sarcopterygian fish Latimeria, identifying 17 2015). On the other hand, the Mu ¨ llerian duct develops in new genes (table 1 and supplementary table 6, female coelacanths and lungfish (Hildebrand and Goslow Supplementary Material online) in addition to those investi- 2001) and in a basal group of actinopterygian fishes, the gated in our previous work (Forconi et al. 2013). The expres- sturgeons (Wrobel 2003). In lungfish and in the teleosts, sion levels (absent, low, intermediate, high) of the identified amh is preferentially expressed in male gonads and a robust genes were compared between the two basal sarcopterygians expression of this gene could be also observed in the testis of andwiththe teleosts Danio rerio and Oryzias latipes to provide Latimeria (table 2). the basis for a better understanding of the gene regulatory Like coelacanth and most other fish, lungfish possess a network governing gametogenesis and sex differentiation bona fide ortholog of amhr2 (supplementary fig. 2, and their evolution. Supplementary Material online). Unexpectedly, this gene is missing in the zebrafish genome. This appears to be species-specific feature, as amhr2 orthologs are present in Growth Factors and Their Receptors other teleost genomes. In medaka, amhr2 is highly expressed Anti-Mu ¨ llerian hormone (Amh), also known as Mu¨llerian in testis (supplementary fig. 1, Supplementary Material on- duct-inhibitory substance, is a member of the transforming line), and mutation of this gene leads to overproliferation of Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1433 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE Table 2 Growth Factors and Receptors Generally Related to Male Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary amh þ þ N.R. þþþþ  þþ þ amhr2 þ þ N.R. Absent þþ þ gsdf þ þ N.R. þþþþ þ þþþþ þþ fgf9 þ  N.R. Absent Absent fgf16 þ  N.R. fgf20a Absent  N.R. fgf20b þ fgf24 Absent  N.R. þþþ sdf1a þþþþ þ þ N.R. þþþ  þ þ sdf1b þ  þþ þ cxcr4a þþþþ þ þþ N.R. þþþþ cxcr4b þþ þþ a a pdgfaa þ þ þ N.R. þ pdgfab þ pdgfra þ þ N.R. þþþ pdgfb þ þ N.R. þþ pdgfrb þþ  N.R. þþþ Approximately 3-fold higher in ovary than testis. the germ cells in both testis and ovary, showing an important gene was already present in the common ancestor of role of Amh signaling in germ cell proliferation in adult gonad Chondrichthyes and Osteichthyes. (Morinaga et al. 2007). This gene is expressed in the testis of The high expression of gsdf in P. annectens testis (table 2)is Latimeria, whereas in the lungfish its expression is only found in line with data previously observed in coelacanth (Forconi in female gonads (table 2). This finding supports the presence et al. 2013) confirming the important role of this gene for of female expression bias of amhr2 in lungfish, like in tetra- male gonad development also in basal sarcopterygians. pods (Fagerberg et al. 2014; Jansson et al. 2016), but not in Furthermore, this pattern is in accordance with the well- Latimeria,where amhr2 is exclusively expressed in testis, like in described dimorphic expression of this gene in other fish spe- teleost fish, where a reverse organ expression pattern has cies (Kaneko 2015). gsdf can even act as master sex deter- been observed (Lubieniecki et al. 2015). mining gene (Myosho et al. 2012; Zhu et al. 2016)or as a Gonadal Soma-Derived Factor (GSDF) is another member male sex initiator, being activated by Dmrt1/Dmy (Zhang et al. of the TGF-b superfamily. This gene is particularly interesting 2016). because of its crucial function in fish testis development In summary, our results point out that a gsdf gene with (Zhang et al. 2016). Prior to our identification of a homolo- testis-specific function was retained in the sarcopterygian gous sequence in Latimeria (Forconi et al. 2013), gsdf was ancestors of tetrapods, only to be lost during the transition hypothesized to be a teleost innovation. Here, we report a from water to land. transcript encoding for gsdf also in P. annectens,whose R-spondin1 (Rspo1) is a regulator of the WNT/b-catenin orthology assessment is strongly supported by phylogenetic signaling pathway. This gene has been characterized as a fe- inference (fig. 2A). Moreover, as a distinctive feature, Gsdfs male sexual regulator in mammals, as it suppresses the male lack a glycine residue in the CxGxC motif, different from Inha axis and maintains oocyte survival by positively regulating and Amh proteins which have this amino acid (fig. 2B). The WNT4 signaling. In tetrapods and several teleosts, rspo1 presence of glycine in this motif is essential for heterodimer shows a sexually dimorphic expression pattern with higher formation of glycoprotein hormones (Kinoshita et al. 2006). values in the female gonad (Zhou et al. 2016), suggesting The functional meaning of this amino acid change for Gsdf is that Rspo1/Wnt/b-catenin signaling is an ancient pathway unknown, due to the lack of information about the signaling of ovarian differentiation in vertebrates. We found a quite pathway of this gene. The identification of a gsdf sequence in high expression for rspo1 in lungfish testis (table 3), and P. annectens implies its subsequent loss in the tetrapod line- much lower levels in ovaries. In zebrafish, rspo1 is equally age. Moreover, the additional identification of a gsdf se- expressed in ovary and testis, while in medaka no expression quence in the cartilaginous fish C. milii evidences that this was detected. rspo1 is also expressed in the ovary and testis of 1434 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.2.—Gsdf phylogeny. (A) Phylogenetic tree of Gsdf, Amh, and Inha amino acid sequences. Bayesian inference: 2,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.007, burn-in set to 5,000, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. (B) Multiple alignment of Gsdf, Amh, and Inha amino acid sequences showing the CxGxC conserved motif and the lack of the glycine residue, which is diagnostic for Gsdf proteins. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1435 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE Table 3 Growth Factors and Receptors Generally Related to Female Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary dhh þþ N.R. þ  þþ ptch2  N.R. þ þ hhip þ N.R. þþ þ þ þ ctnnb1 þþþ þþþþ þþþ N.R. þþþþ þþþþ þþþ þþ fst þ N.R. þ þ a a wnt4a þ N.R. þ þ a a wnt4b þ þ þ rspo1 þþ þ þ N.R. þþ Approximately 2- to 3-fold higher in testis than ovary. other teleosts, suggesting that it might be involved in both of fgf9 in C. milii dates back the origin of this gene to the ovarian and testicular development and spermatogenesis (Wu common ancestor of Chondrichthyes and Osteichthyes, im- et al. 2016). In other vertebrates, RSPO1 is widely expressed plying its loss in the lineage of Actinopterygii. Neither fgf9 nor (Han et al. 2015) and its transcript has been also detected in the other members of the FGF9/16/20 subfamily are adult human testis (Parma et al. 2006). Our findings suggest expressed in testis of lungfish and coelacanth (table 2). In that theroleof rspo1 in lungfish male gonads is not con- lungfish, we verified the absence of fgf20 both at the tran- nected to the action of wnt4, asthisgene is poorly expressed scriptome level. Moreover, fgf9 is strongly expressed in lung- in lungfish and coelacanth, while both wnt4 co-orthologs are fish ovary (table 2). This may indicate that the important well expressed in the gonads of zebrafish. Medaka, on the function of fgf9 for testis development is an innovation ac- other hand, presents relatively low expression of wnt4b in quired after the transition from water to land. testis. To evaluate the possible involvement of another member ß-catenin (Ctnnb1) is the critical molecule that transmits of the FGF gene family as a functional homolog of the tetra- the activity of the female determining pathway signals of pod Fgf9, as recently proposed by Leerberg et al. (2017),we Wnt4 and R-spondin to the nucleus to activate effector genes. took a closer look at fgf24, a member of the FGF8/17/18/24 High expression values were recorded for ctnnb1 in all four family (fig. 4). The isolation of this gene in the elephant shark species (table 3). While no strong sex bias in expression is supported its presence in the common ancestor of gna- present in zebrafish and medaka, the lungfish ovary shows thostomes (Jovelin et al. 2010). Within the sarcopterygian considerably higher levels than testis, in contrast with the ex- lineage, fgf24 could be only identified in Latimeria pression pattern of wnt4 and rspo1 (table 3). (Amemiya et al. 2013) but not in tetrapods (Jovelin et al. Follistatin (Fst) encodes a TGFß superfamily binding protein 2010). In addition, no orthologous sequence to fgf24 that acts downstream of WNT4 to maintain germ cell survival could be retrieved from the P. annectens transcriptome, in the cortical domain of the mammalian ovary (Yao et al. which might either indicate the lack of expression of this 2004). This gene is present in both basal sarcopterygians. The gene, or its loss. If confirmed at the genome level, this lack expression of fst in lungfish, in line with the absence of finding might indicate that fgf24 was lost in the common detectable expression for wnt4 (table 3), may be connected to ancestor of lungfish and tetrapods. This gene is expressed the prereproductive stage of the female gonads. in the early somatic and in adult gonads of zebrafish Fibroblast Growth Factors (Fgf) are a family of small pro- Leerberg et al. (2017) (table 2) and was suggested as a teins that have multiple functions in regulating cellular devel- plausible candidate to substitute for fgf9 function in tele- opment and growth. Numerous studies in mice have shown osts. In addition, fgf24 is expressed only in testis of adult that FGF9 plays an important role in testis development, cre- medaka. ating a positive feedback loop with Sox9 and antagonizing Stromal-cell-derived factor 1 (Sdf1, also known as Cxcl12) Wnt4, an ovarian factor (Jameson et al. 2012). No orthologs is a chemokine involved in a wide variety of body functions. It of fgf9 have been identifiedinactinopterygian fishsofar (Itoh binds to CXC receptor 4 (Cxcr4), a G-coupled transmembrane and Konishi 2007). The identification of fgf9 in Latimeria has glycoprotein located on the surface membranes of primordial previously suggested that this gene was present in the com- germ cells. The interaction between Sdf1 and its receptor mon ancestor of Sarcopterygii (Forconi et al. 2013), a hypoth- regulates migration and proliferation of various cell types, esis which is now further supported by the retrieval of this which importantly comprise also teleosts primordial germ sequence also in P. annectens (fig. 3). Moreover, the presence cells. Previous studies assigned a central role to Sdf1 and 1436 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.3.—Fgf9/16/20 phylogeny. Phylogenetic analysis of Fgf9, Fgf16, Fgf20. Bayesian inference: 1,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.0055, burn-in set to 2,500, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. CXCR4 in the development of embryonic and postnatal go- Steroidogenic Enzymes nad (Yang et al. 2013; Westernstro ¨ er et al. 2014; Fernandez Steroid-5-Alpha-Reductase Alpha Polypeptides 1, 2, 3 et al. 2015). In human adults, the expression of SDF1 was (Srd5a1, Srd5a2, Srd5a3) are proteins involved in the conver- observed in Sertoli cells. The expression of Cxcr4 in adult sion of testosterone to dihydrotestosterone (DHT), a very po- mouse testis (Yang et al. 2013) further suggests a role for tent androgen in teleosts fishes and tetrapods. Unexpectedly, the ligand/receptor in spermatogenesis. Both genes are pref- we detected higher expression of srd5a1 in lungfish ovary, in erentially expressed in lungfish male gonads (table 2), at par- contrast to its absence in zebrafish and the low expression in ticularly high levels in the more immature testis sample. In female medaka (supplementary table 7, Supplementary addition, the expression of these genes has been also recently Material online). Srd5a1 is predominantly expressed in the reported in both male and female gonads of the teleost female gonads of frogs but also in rat (Lephart et al. 1992) Oreochromis mossambicus (Amat-Fernandez et al. 2017). and human (Haning et al. 1996; Mahendroo and Russell Platelet-derived growth factors (Pdgf) and their receptors 1999), consistently with our observations in lungfish (supple- are involved in regulating the development of various tissues mentary table 7, Supplementary Material online). This finding (Miura et al. 2002). In particular, they play a fundamental role suggests that Srd5a1 might confer the ability of metabolizing in the development of gonadal tissue in mammalian fetal and testosterone into DHT in the sarcopterygian lineage, while a adult testis (Li et al. 2016). In zebrafish and medaka, this gene different isozyme is likely used in teleost fish. is preferentially expressed in testis (table 2). However, in both Cytochrome P450 19A1 (Cyp19a1 or aromatase) cata- sarcopterygians, the expression of pdgfs and their receptors in lyzes the final step in the biosynthesis of estrogens, which testis were quite low. The lungfish pdgfa and pdgfrb ortho- have a key role in ovarian differentiation and maintenance logs unexpectedly showed the highest expression levels in in fish, amphibians, reptiles, and birds (Bruggeman et al. ovary (table 2). Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1437 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE FIG.4.—Fgf8/17/18/24 phylogeny. Phylogenetic analysis of Fgf8, Fgf17, Fgf18, Fgf24. Bayesian inference: 2,000,000 generations, sampling every 100, Jones substitution model, stationarity defined as when the average SD of split frequencies approaching 0.0062, burn-in set to 5,000, midpoint rooting. Numbers close to nodes indicate posterior probability values. Only values >95 were reported. The sequences in bold were obtained in this work. 2002; Dumond et al. 2008; Lubieniecki et al. 2015). The detect 11-ketotestosterone in Australian lungfish (Joss et al. expression patterns observed in the present study is con- 1996). sistent with a conserved function for this gene also in basal sarcopterygians (supplementary table 8, Steroid Hormone Receptors Supplementary Material online). Cytochrome P450 11c1 (Cyp11c1). In most teleost fish the The expression of steroidogenic enzymes is usually connected predominant androgen is 11-ketotestosterone, which is pro- to the production of biologically active estrogens and andro- duced from testosterone by the action of the cyp11c1 gene. gens. The action of these steroid hormones requires the pres- However, tetrapod cyp11B homologs function predominantly ence of the cognate receptors, whose transcription is often in adrenal steroid biosynthesis and are not expressed in testis further up-regulated by the presence of hormones in a posi- (Schiffer et al. 2015). A gene pertaining to the CYP11 sub- tive feedback loop. We found a very unexpected expression family is present in lungfish as well as in the coelacanth (sup- pattern for these receptors in lungfish. Indeed, while the an- plementary fig. 3, Supplementary Material online). The drogen receptor (ar) was expressed in the mature testis of absence of expression in the gonads of these two species is coelacanth and teleost, no expression could be detected in in line with the results of a previous study, which failed to lungfish male gonad nor in any other tissue (supplementary 1438 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE Table 4 Transcription Factors Generally Related to Male Sex Determination, Differentiation, and Reproductive Functions Lungfish Coelacanth Zebrafish Medaka Testis Ovary Testis Ovary Testis Ovary Testis Ovary dmrt1 þþ þ þþ N.R. þþþþ þ þþ þ dmrt3  N.R. þ þ dmrt6 þþ þ þþþ N.R. Absent Absent sox3  N.R. þ þ sox5 þ N.R. þþþ   þ sox8a þ N.R. þþþ sox8b þþþþ þ a a sox9a þ þ þþ N.R. þ þ þ b b sox9b þ þ þ sox10 þ N.R. þ gata4 þþ N.R. þ þ þ lrpprc þþ þþþ þþ N.R. þþþ þþþ þ þþ sf1 þþþ þ þ N.R. þþþþ þþþþ þþ þ wt1a þþ N.R. þþ þ þ þ wt1b þþ pax2a þ N.R. þ pax2b þ In ovary barley above background, but robust expression in testis. Approximately 3-fold higher in ovary than testis. table 7, Supplementary Material online). Whether this ab- Although no dmrt6 gene has been annotated yet in any of the sence is linked to the nonreproductive stage of the gonads fully sequenced teleost genomes, a recent publication or to the use of another nuclear receptor for sensing andro- reported dmrt6-like sequences in spotted gar, cichlids, and gen levels in lungfish remains an interesting question to be siluriforms. This dmrt6-like gene was expressed in spermato- approached in the future. Teleost esrs were also preferentially cytes and its function was shown to be involved in spermato- expressedintestis(supplementary table 8, Supplementary genesis in tilapia (Zhang, Wang, et al. 2014). The loss of this Material online). On the other hand, mammalian ESRsare gene in some teleost lineages could represent another aspect produced at very low levels in testis (Cavaco et al. 2009). of the extreme variability of the genetic network involved in The exceptionally high levels identified in lungfish male sex determination and differentiation in fish. Overall, the pres- gonads may be related to the premature status of the tissues ence and expression of dmrt6 in basal sarcopterygians sup- available for this study (supplementary table 7, Supplementary ports an ancient and conserved function for this gene in testis Material online). development and function. The Steroidogenic Factor 1 (Sf1) was mainly expressed in lungfish and coelacanth testis, while in zebrafish it showed a Transcription Factors broader tissue distribution (table 4). Sf1 is expressed in both sexes in mice fetal gonads, but in later developmental stages it Doublesex- and mab-3-related transcriptional factor 1 continues to be expressed only in testes, where it is activated (Dmrt1), together with Amh and Sox9, is important for ver- and maintained by Wilms tumor 1 (WT1). On the other hand, tebrate testicular differentiation. Its expression of dmrt1 in Sf1 is down-regulated by Forkhead box L2 (FOXL2) in ovary lungfish (table 4) is in agreement with the dimorphic expres- (Takasawa et al. 2014). The low expression of sf1 observed in sion pattern observed from fish to mammals (Websteretal. lungfish ovary, opposed to the high expression detected in 2017) and suggest a major role in adult testis function. zebrafish female gonad, is in line with the mammalian In contrast to other vertebrates (Bratus and Słota 2009), no pattern. trace of dmrt3 expression was detected in the two basal sar- SRY-related HMG box (SOX) family proteins are transcrip- copterygians (table 4). On the other hand, the expression of tion factors involved in many developmental processes. In dmrt6 in lungfish and coelacanth testis is intriguing (table 4). particular, sox3, sox5, sox8, sox9,and sox10 have a function In mice, this gene is likely involved in directing the transition in gonad development. SOX3 belongs to subfamily B and from spermatogonia to spermatocytes (Zhang, Murphy, et al. is the ancestor of SRY (Marshall-Graves 2008). Although 2014). This study allows to extend the taxonomic range dis- sox3 is not required for sex determination in mammals tribution of dmrt6 from tetrapods to basal sarcopterygians. Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1439 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE (Weiss et al. 2003), it is the master male sex determining gene in the fish Oryzias dancena (Takehana 2014). sox5, pertaining to the subfamily D, is a regulator of male germ cells in medaka (Schartl et al. 2018). It is expressed in mice postnatal testis and, together with Sox9 and Sox13, it may play a role in spermatogenesis (Daigle et al. 2015). The other three genes belong to subfamily E: SOX9 is activated by SRY in mammals and is required for sex determination in tetrapods (Jakob and Lovell-Badge 2011); whereas Sox8 is activated by SOX9 and acts in a positive feedback loop on Sox9 in testis differentia- tion, as shown in mice. All five sox genes are present in the lungfish transcriptome. In Latimeria, in addition to the sox8/9/ 10 sequences identified in our previous work (Forconi et al. 2013), we can report the identification of sox3 (from the ge- nome) and sox5 (from transcriptome data). The orthology status of the isolated sequences was assessed by phylogenetic analysis (supplementary fig. 4, Supplementary Material online) FIG.5.—Stra8 phylogeny. Phylogenetic analysis of Stra8. Bayesian that assigned each sequence to the corresponding sox gene inference: 1,000,000 generations, sampling every 100, Jones substitution clade. model, stationarity defined as when the average SD of split frequencies The tissue distribution of sox3 transcripts confirms that the approaching 0.0033, burn-in set to 2,500, midpoint rooting. Numbers almost exclusive role of this gene in brain is also retained in close to nodes indicate posterior probability values. Only values >95 basal sarcopterygians (table 4). Together with SOX1 and were reported. The sequences in bold were obtained in this work. SOX2, the other two paralogs of the B1 group of the SOX family, SOX3 plays a key role in central nervous system devel- coelacanth, lungfish, and zebrafish. Expression of foxl3 in opment in mouse (Rogers et al. 2013). sox8 was neither the gonad was observed only in medaka, indicating a diver- expressed in Latimeria (Forconi et al. 2013) nor in lungfish gent role of this gene between different vertebrates. This testis (table 4). In mammals, the action of SOX8 in the gene has not been identified in placental mammals and in FGF9/SOX9 interaction loop is important for testis mainte- amphibians (Bertho et al. 2016) and, except from the study in nance (Barrionuevo et al. 2009). The lack of expression of medaka, its gonadal function remains unclear. both sox8 and fgf9 hints that this interaction loop, which is crucial in mammalian sex determination, is not yet in place in Meiosis Regulation Genes basal sarcopterygians. Both sox9 and wt1 are expressed in lungfish and coelacanth testis, in line with their known pat- Meiosis is one of the most important processes in sexual re- tern of distribution in tetrapods. production, as it produces haploid gametes. However, regu- Forkhead transcription factors (Fox) are involved in many lation of the meiotic program is still insufficiently understood biological processes, including the regulation of cell prolifera- in most species. In mammals, the morphogen retinoic acid tion and differentiation, tissue development, and various met- triggers meiotic entry through up-regulation of the abolic processes. Foxl2 plays a key role in the early Stimulated by retinoic acid gene 8 (Stra8). This gene encodes development of vertebrate female gonads and, in adults, a retinoic acid-responsive protein that plays a critical role in has an ovarian function. In particular FOXL2 suppresses the regulation of meiotic initiation during spermatogenesis Dmrt1 for maintaining female fate (Matson et al. 2011) and oogenesis (Feng et al. 2014). Commonly present in tetra- and, together with WNT4, cooperates in regulating Fst ex- pods, this gene is absent in some teleosts species, including pression during ovarian development (Garcia-Ortiz et al. zebrafish (Rodrıguez-Marı et al. 2013). A more comprehen- 2009). It regulates estrogen synthesis via up-regulation of sive analysis of the evolution of stra8 suggests that this gene Cyp19A1a (Pannetier et al. 2006). In medaka, the paralogous was lost in Acanthomorpha and, independently, in the gene foxl3 encodes a protein that may play a role in sexual Cypriniform lineage within Actinopterygii (Pasquier et al. fate decision in germ cells by suppressing spermatogenesis 2016). We can however report the presence of this gene in (Nishimura et al. 2015). While both these genes are present the two basal sarcopterygian species. Phylogenetic analysis in the genome of L. chalumnae, only foxl2 was found in the P. positioned the lungfish and coelacanth sequences at a basal annectens transcriptome. The sequences identified were used position compared with tetrapods (fig. 5). for phylogenic analyzes (supplementary fig. 5, Supplementary The level of the retinoic acid as a meiosis signal is deter- Material online). foxl2 was expressed in lungfish female mined by the antagonistic action of enzymes involved in its gonads (supplementary table 9, Supplementary Material on- synthesis and degradation: the enzyme ALDH1a2, a member line). No expression of foxl3 was however detected in of the retinaldehyde dehydrogenase family, is responsible for 1440 Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Sex Genes in Lungfish and Coelacanth GBE FIG.6.—Summarizing scheme of sex-related genes lost in the main vertebrate lineages. The scheme shows the sex genes lost in tetrapods, lungfish, coelacanth, and teleosts. The colours are referred to the functional groups, respectively. its synthesis, while CYP26B1 encodes a major retinoic acid- (supplementary table 2, Supplementary Material online). All degrading enzyme. In mice, down-regulation of Cyp26b1 in genes appear to evolve under purifying selection (Ka/Ks<1) femalesleadstohighlevels of retinoic acid, whichin turn with the exception of the x rate obtained between the two induce the expression of the premeiotic marker Stra8, thereby gsdf co-orthologs in D. rerio. allowing female germ cells to enter meiosis. Cyp26b1 acts as a Our analysis of lungfish ovary and testis transcriptomes and meiosis-inhibiting factor in mammals, birds, and amphibians the comparison with similar data sets from both zebrafish and (Bowles and Koopman 2010; Piprek, Pecio, Laskowska- medaka, and with the testis transcriptome of coelacanth Kaszub, Kloc, et al. 2013; Yu et al. 2013), while in teleosts revealed a situation that reflects the peculiar phylogenetic this role is exerted by cyp26a1 (Adolfi et al. 2016). position of the Dipnoi. We identified some genes whose ex- We found high expression of cyp26b1 and stra8 in pression pattern in lungfish and, as far as testis is concerned, lungfish and coelacanth male gonads suggesting that also in Latimeria is more similar to teleosts than tetrapods. As basal sarcopterygians follow the tetrapod pattern (sup- an example, gsdf, which is an important male determining plementary table 10, Supplementary Material online). gene in teleosts, but which is missing in the tetrapod lineage, However, significant differences were observed in the was present and highly expressed in testis of both lungfish expression of aldh1as: aldh1a1 showed higher expres- and coelacanth. sion in lungfish male gonads, and is therefore the only On the other hand, a number of other genes present in gene responsible for retinoic acid synthesis in coelacanth lungfish display a behavior more similar to tetrapods than testis (supplementary table 10, Supplementary Material teleost fishes, for example, srd5a1, which was highly online). Such lineage specific subfunctionalization of ret- expressed in lungfish ovary, like in tetrapods, or b-catenin, inoic acid metabolizing enzymes has also been reported the transcription factor readout of the female gonad spe- in a comparative study among different teleost fish cific tetrapod signaling cascade, which was also highly (Canestro et al. 2009). cyp26c1 was not found in the expressed in lungfish ovary. Intriguingly, the upstream ef- lungfish transcriptome, marking a possible lineage- fector R-spondin1 does not follow this pattern. At the specific loss. same time wnt4, which is an ovary specific gene in tetra- pods and an upstream regulator of ß-catenin, is highly expressed in teleost testis and did not show significant Conclusions expression in lungfish and coelacanth gonad samples. Our analysis of sex differentiation and gametogenesis genes Sf1 is a male specific gene in mammals and lungfish go- in lungfish and coelacanth revealed a complex picture. None nad, which was also highly expressed in Latimeria testis. of the gene-encoded protein products showed any unusual stra8 is absent from many major teleost lineages, but it is structural feature, like missing or additional domains or unex- present and highly expressed in the testis of basal sarcop- pectedly high sequence divergence. We calculated the x rates terygians, following the tetrapod profile. Dmrt6, a gene for genes that were of special interest due to their appear- which has an important function in mammalian spermato- ance/disappearance at the split of sarcopterygians and actino- genesis and which is only seldom found in teleost pterygians (fgf9, foxl3, gsdf,and stra8), in lungfish, genomes, showed high expression in lungfish and coela- coelacanth and other representative vertebrates canth testis, indicating functional conservation. The Genome Biol. Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 1441 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Biscotti et al. GBE reasons underpinning the possible loss of such an impor- the conception of the study and the experimental design and tant gene in most teleosts—similar but independent from have given final approval for the version to be published. stra8—are totally unclear. Finally, some lungfish and coelacanth genes follow nei- Literature Cited ther the teleost nor the tetrapod scheme. Fgf9 is an im- Adolfi MC, Herpin A, Regensburger M, Sacquegno J, Waxman JS. 2016. portant male sex determining gene in tetrapods, which is Retinoic acid and meiosis induction in adult versus embryonic gonads absent in teleosts. Our analysis demonstrates that fgf9 has of medaka. Sci Rep. 6:34281. been specifically lost in the teleost lineage and the ab- Amat-Fernandez J, et al. 2017. 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Evol. 10(6):1430–1444 doi:10.1093/gbe/evy101 Advance Access publication May 29, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1430/5020732 by Ed 'DeepDyve' Gillespie user on 20 June 2018

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