Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii

Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii Genome reduction is a recurring theme of symbiont evolution. The genus Spiroplasma contains species that are mostly facultative insect symbionts. The typical genome sizes of those species within the Apis clade were estimated to be 1.0–1.4 Mb. Intriguingly, Spiroplasma clarkii was found to have a genome size that is>30% larger than the median of other species within the same clade. To investigate the molecular evolution events that led to the genome expansion of this bacterium, we determined its complete genome sequence and inferred the evolutionary origin of each protein-coding gene based on the phylogenetic distribution of homologs. Among the 1,346 annotated protein-coding genes, 641 were originated from within the Apis clade while 233 were putatively acquired from outside of the clade (including 91 high-confidence candidates). Additionally, 472 were specific to S. clarkii without homologs in the current database (i.e., the origins remained unknown). The acquisition of protein-coding genes, rather than mobile genetic elements, appeared to be a major contributing factor of genome expansion. Notably,>50% of the high- confidence acquired genes are related to carbohydrate transport and metabolism, suggesting that these acquired genes contributed to the expansion of both genome size and metabolic capability. The findings of this work provided an interesting case against the general evolutionary trend observed among symbiotic bacteria and further demonstrated the flexibility of Spiroplasma genomes. For future studies, investigation on the functional integration of these acquired genes, as well as the inference of their contribution to fitness could improve our knowledge of symbiont evolution. Key words: mollicutes, Spiroplasma, symbiont, comparative genomics, horizontal gene transfer (HGT). Introduction mutualists of insects, which have genome sizes in the The patterns of genome evolution among diverse symbi- range of 0.1–1.0 Mb (Moran and Bennett 2014). otic bacteria are characterized by a general trend of ge- The genus Spiroplasma within the class Mollicutes contains nome reduction (Moran and Plague 2004; Ochman and diverse species that are mostly facultative insect symbionts Davalos 2006; Toft and Andersson 2010; McCutcheon capable of horizontal transmission (Gasparich et al. 2004; and Moran 2012; Moran and Bennett 2014). This obser- Regassa and Gasparich 2006; Gasparich 2010). In recent vation is likely a combined result of the mutational bias years, these bacteria have been developed into a model sys- towards deletions commonly observed in bacteria (Mira tem for the study of symbionts (Anbutsu and Fukatsu 2011; et al. 2001; Kuo and Ochman 2010), the lack of selection Bolanos et al. 2015; Lo et al. 2016). This paraphyletic genus against gene losses in stable and nutrient-rich environ- contains several major clades, with the Apis clade as the most ments, and the elevated levels of genetic drift due to genetically diverse and species-rich one. Based on the genome host restriction (Kuo et al. 2009; Novichkov et al. 2009). size estimates by pulsed-field gel electrophoresis (PFGE), most Although most free-living bacteria have a genome size of these Spiroplasma species haveagenomesizeof 1.0– that is>4 Mb, symbionts usually have a smaller genome. 1.4 Mb (Carle et al. 1995). Given these general observations, The most extreme examples of genome reduction were it is interesting to note that Spiroplasma clarkii, a facultative found among those obligate intracellular nutritional symbiont residing in the gut of larval/adult Scarabaeidae 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 1526 Genome Biol. Evol. 10(6):1526–1532. doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE beetles without apparent effect on its host, was found to have a genome size that is>30% larger than the median of other species within the same clade (Whitcomb et al. 1993). To investigate the evolutionary processes and the genetic changes that led to the genome expansion in this bacterium, we determined the complete genome sequence of S. clarkii for comparative analysis. Materials and Methods The procedures for genome sequencing and phylogenetic in- ference were based on those described in our previous studies (Lo,Chen, et al.2013; Lo, Ku, et al. 2013; Chang et al. 2014; Lo et al. 2015). The bioinformatics tools were used with the default settings unless stated otherwise. Briefly, the bacterial strain Spiroplasma clarkii CN-5 was acquired from the German Collection of Microorganisms and Cell Cultures (catalogue number: DSM 19994 ). For whole-genome shotgun sequenc- ing, one paired-end library (550 bp insert and 430X coverage) and one mate-pair library (4.5 kb insert and 60X coverage) were prepared and sequenced using the MiSeq platform (Illumina, USA). The de novo assembly was performed using ALLPATHS-LG release 52188 (Gnerre et al. 2011), followed by gap closure and validation using PCR and Sanger sequencing until the complete sequence of the circular chromosome was obtained. The programs RNAmmer (Lagesen et al. 2007), tRNAscan-SE (Lowe and Eddy 1997)and PRODIGAL (Hyatt et al. 2010) were used for gene prediction. The annotation was based on the homologous genes in other Spiroplasma genomes (supplementary table S1, Supplementary Material on- line) as identified by OrthoMCL (Li et al. 2003), followed by manual curation based on the KEGG (Kanehisa et al. 2016) and COG databases (Tatusov et al. 2003). To identify the homologs of protein-coding genes in other bacteria for each Apis clade species, we performed BLASTP (Camacho et al. 2009) search against the NCBI nonredundant database (version date: March 26, 2018). After removing the self-hit and low-quality hits (i.e., high-scoring pairs accounting for<90% of the query length or amino acid sequence sim- ilarity<40%), uptofive tophits were collected for eachquery (supplementary table S2, Supplementary Material online). Representative species from these hits (supplementary table S1, Supplementary Material online) were selected for an addi- tional round of homologous gene identification by OrthoMCL. Putatively acquired islands, defined as regions that have at least FIG.1.—Continued FIG.1.—Maximum likelihood phylogenies of representative lineages. species identified in the homologous gene search. The bootstrap support (A) A phylogram of the Apis clade based on a concatenated alignment of for each major clade is labeled above the branch; internal branches with a 412 single-copy genes and 148,728 aligned amino acid sites. All nodes bootstrap support below 80% were collapsed. Species highlighted with received>95% bootstrap support. The numbers in parentheses indicate “*” are those with genome sequences available and included in the iden- the chromosome size (unit: Mb) and the number of protein-coding genes. tification of horizontally transferred gene islands. All accession numbers (B) A cladogram based on the 16S rDNA phylogeny of the representative are provided in supplementary table S1, Supplementary Material online. Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 1527 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Tsai et al. GBE FIG.2.—Chromosomal organization of S. clarkii. Concentric circles from the inside out: 1) GC content (above average: dark gray; below average: light gray; two high GC peaks near the 0.5 Mb mark correspond to the rRNA gene clusters), 2) GC skew (positive: dark gray; negative: light gray), 3) locations of the high-confidence candidates of acquired genes (colored in red; putatively acquired islands with at least five genes from the same donor are highlighted with a pink background), 4–8) phylogenetic affiliations of the top five BLASTP hits from the NCBI nonredundant database (color-coded according to the legend), and 9) scale marks (unit: Mb). five acquired genes and exhibit synteny conservation with spe- species among all hits and processed using the same procedure. cies outside of the Apis clade, were identified. For the inference of individual gene trees, we relaxed the criteria For maximum likelihood phylogenetic analysis, two species for filtering out low quality BLASTP hits (i.e., high-scoring pairs phylogenies were inferred. The first one was focused on the accounting for<80% of the query length or amino acid se- Apis clade, the amino acid sequences of the shared single-copy quence similarity<30%) in an attempt to identify more distant genes were extracted from the OrthoMCL results used for an- homologs. Putatively acquired genes in S. clarkii with at least notation. The multiple sequence alignment was performed us- five homologs from other Apis clade species among the top 100 ing MUSCLE v3.8 (Edgar 2004) for each gene. The hits were selected for phylogenetic analysis using the same pro- concatenated alignment was analyzed using PhyML v3.0 cedure. The GenBank accession numbers for all of the sequen- (Guindon and Gascuel 2003). The proportion of invariable sites ces included in the phylogenetic analysis are provided in and the gamma distribution parameter were estimated from supplementary table S1, Supplementary Material online. the data set, the number of substitute rate categories was set to four. The bootstrap supports were estimated based on 1,000 Results and Discussion replicates. The second species phylogeny with broader taxon The complete genome sequence of S. clarkii contains one sampling was based on the BLASTP search result. The 16S circular chromosome that is 1.56 Mb in size; no plasmid rDNA sequences were extracted from the representative 1528 Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE Table 1 Classification of Protein-Coding Genes by Putative Origins Genome Apis Species-Specific HGT-Low Confidence HGT-High Confidence S. clarkii 641 (48%) 472 (35%) 142 (11%) 91 (7%) S. helicoides 679 (68%) 198 (20%) 99 (10%) 21 (2%) S. culicicola 709(66%) 228 (21%) 98(9%) 36(3%) S. apis 728 (63%) 281 (24%) 109 (10%) 33 (3%) S. turonicum 780 (73%) 149 (14%) 115 (11%) 20 (2%) S. corruscae 667(69%) 218 (22%) 70(7%) 18(2%) S. litorale 789 (74%) 151 (14%) 105 (10%) 21 (2%) S. cantharicola 745 (73%) 123 (12%) 104 (10%) 45 (4%) S. diminutum 770 (76%) 119 (12%) 115 (11%) 4 (0%) S. taiwanense 728 (85%) 50 (6%) 67 (8%) 13 (2%) S. sabaudiense 243 (26%) 338 (37%) 178 (19%) 165 (18%) NOTE.—Values indicate the gene count; the percentage of total is provided in parentheses. Due to the high level of sequence divergence from other Apis clade species, as well as its basal placement in the species phylogeny, this approach of utilizing BLASTP searches to classify the putative origin of genes is not applicable to S. sabaudiense. These values are provided for reference only and are not included in the calculation of average percentages among Apis clade species as discussed in the main text. was found. Although this size is 12% smaller than the group based on the same procedure and on average those 1.77 Mb estimate based on PFGE (Whitcomb et al. 1993), it species-specific genes account for only 16% of the total is still>30% larger than the median of other Apis clade spe- gene count in other Apis clade species. Unfortunately, al- cies with complete genome sequences available (fig. 1A). though the hypothesis that most of these species-specific Moreover, comparison between the actual genome size of genes were acquired through HGT is plausible, direct evidence these species with previous estimates (Carle et al. 1995; for or against this hypothesis is lacking. The remaining genes Williamson et al. 1996; Whitcomb et al. 1997; Helias et al. were assigned to two classes of HGT candidates, including 1998) revealed that the PFGE method typically overestimates 142 low-confidence ones (i.e., the top five hits involved a thegenomesize by 10–15%. mixture of species from within the Apis clade and other Examination of the chromosome organization and gene more divergent ones; 11% of the count and 9% of the content (fig. 2) revealed that the genome expansion was length) and 91 high-confidence ones (i.e., the top five hits not attributed to the invasion of plectroviruses as those found did not involve any Apis clade species; 7% of the count and within the Spiroplasma Citri clade, in which viral sequences 6% of the length). The low confidence candidates may in- account for 20% of the chromosome in extant species clude those acquired prior to the divergence between S. clarkii (Carle et al. 2010; Alexeev et al. 2012; Ku et al. 2013; Lo, and Spiroplasma helicoides, or those with more complex his- Chen, et al. 2013; Paredes et al. 2015). Rather, acquisition of tory such as multiple gain/loss events. However, due to the protein-coding genes through horizontal gene transfer (HGT) limited number of homologs available in the current database, appeared to be a major factor. Among the 1,346 annotated as well as the finding that many of these low confidence protein-coding genes, 641 (48% of the gene count and 45% candidates correspond to short hypothetical proteins, it is dif- of the chromosome length) were inferred as being originated ficult to infer the exact evolutionary history of these genes. from within the Apis clade (table 1). For these genes, the top Furthermore, because those low confidence candidates ac- five BLASTP hits within the NCBI nonredundant database did count for 10% of total gene count in other Apis clade spe- not involve any organism outside of the Apis clade, which cies as well, these genes are unlikely to be a main contributing suggested that these genes were either inherited vertically factor of genome expansion in S. clarkii. or at least did not involve recent HGT from donors outside Compared with other Apis clade species, the number and of the Apis clade. There are 472 species-specific genes (i.e., proportion of high-confidence HGT candidates are both those without any identifiable homolog in the current data- much higher in S. clarkii (table 1). This finding further sug- base), which correspond to 35% of the gene count and 29% gested that gene acquisition is a major contributing factor of of the chromosome length. These species-specific genes ap- the genome expansion. Among those 91 high-confidence pear to be the main contributing factor of the genome ex- candidates, 38% were inferred as originated from the sister pansion observed in S. clarkii (table 1). Although some of Mycoides-Entomoplasmataceae clade based on the phyloge- these may be artifacts of gene prediction, we expect that a netic distribution of homologs, whereas those from the Citri- high proportion of these genes may be acquired genes with- Chrysopicola-Mirum clade and other more divergent lineages out known donors. The reason for this inference is that all of within the class Mollicutes account for 13% and 17%, re- these Spiroplasma genomes were annotated by our research spectively (figs. 1B and 3A). Using individual gene phylogenies Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 1529 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Tsai et al. GBE FIG.3.—Classification of the high-confidence candidates of acquired genes. (A) Phylogenetic assignments of the most likely donors. (B) Functional assignments according to the COG categories. FIG.4.—Carbohydrate transport and metabolism. Genes that are putatively involved in horizontal transfer are highlighted by “*” (low-confidence) or “**” (high-confidence; color-coded according to the putative donors). For multicopy genes, subscripts following the gene name are used to distinguish different copies. Abbreviations: DHAP, dihydroxyacetone phosphate; G3P, glycerol-3-phosphate; GlcNAc, N-Acetylglucosamine; MDHA, monodehydroas- corbate; MurNAc, N-acetylmuramic acid. for the test of HGT hypothesis was not feasible for most of homologs in other Apis clade species, we inferred the individ- these candidates; 61 out of these 91 candidates did not have ual gene trees to investigate their evolutionary history (sup- any identifiable homolog in other Apis clade species. plementary fig. S1, Supplementary Material online). At least Although multiple independent losses in all other Apis clade four of these gene trees provided strong support for the HGT lineages may also explain the pattern and argue for vertical hypothesis. inheritance, such alternative hypothesis is less parsimonious Because the vast majority of Entomoplasmataceae/ compared with HGT. For the nine candidates with at least five Spiroplasmataceae species are affiliated with insect hosts for 1530 Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE at leastapartoftheir life cycle (Gasparich et al. 2004; Regassa Acknowledgments and Gasparich 2006; Gasparich 2010; Gasparich 2014), this This work was supported by research grants from the Institute overlap in ecological niche could have promoted the HGT of Plant and Microbial Biology at Academia Sinica and the events among these lineages. Moreover, despite the phyloge- Ministry of Science and Technology of Taiwan [NSC 101- netic divergence, all these Mollicutes lineages share the same 2621-B-001-004-MY3 and MOST 104-2311-B-001-019] to alternative genetic code (i.e., UGA changed from stop to tryp- C.H.K. The funders had no role in study design, data collection tophan) and a strong nucleotide composition bias toward and interpretation, or the decision to submit the work for Aþ T. These shared genomic traits could have promoted publication. The bacterial strain was imported under the per- the retention and integration of those acquired genes (Lo mit number 103-B-001 (Council of Agriculture, Taiwan). The and Kuo 2017). The chromosomal region at 0.9–1.1 Mb Sanger sequencing service and the Illumina sequencing library appeared to be the major hot spot for foreign genes preparation service were provided by the Genomic (fig. 2). A total of 45 genes were identified in seven islands Technology Core Facility (Institute of Plant and Microbial with at least five acquired genes from the same donor with Biology, Academia Sinica). The Illumina MiSeq sequencing synteny conservation. Interestingly, most of the gene acquis- service was provided by the Genomics Core Facility (Institute itions did not disrupt the patterns of GC skew and gene ori- of Molecular Biology, Academia Sinica). We thank Dr. Wen- entation (fig. 2), suggesting that those that did may be Sui Lo for technical assistance. selected against. Regarding the functions, carbohydrate transport and me- tabolism is the most dominant category that accounts for Literature Cited 51% of those high-confidence candidates (fig. 3B). This find- Alexeev D, et al. 2012. Application of Spiroplasma melliferum proteoge- nomic profiling for the discovery of virulence factors and pathogenicity ing is worth noting because carbohydrate metabolism is mechanisms in host-associated spiroplasmas. J Proteome Res. highly variable among Spiroplasma species (Chang et al. 11(1):224–236. 2014; Lo et al. 2015) and is important in their physiology Anbutsu H, Fukatsu T. 2011. Spiroplasma as a model insect endosymbiont. and ecology (Regassa and Gasparich 2006; Gasparich Env Microbiol Rep. 3(2):144–153. 2010). Moreover, carbohydrate metabolism genes are often ~  ~ Bolanos LM, Servın-Garciduenas LE, Martınez-Romero E. 2015. Arthropod–Spiroplasma relationship in the genomic era. FEMS involved in HGT and have been shown to be integrated into Microbiol Ecol. 91(2):1–8. the gene expression regulation in other Apis clade species (Lo Camacho C, et al. 2009. BLASTþ: architecture and applications. BMC and Kuo 2017). Intriguingly, extensive gene acquisition has Bioinformatics 10(1):421. also been reported for Spiroplasma eriocheiris of the Mirum Carle P, Laigret F, Tully JG, Bove JM. 1995. Heterogeneity of genome sizes clade, in which 7% of thegenes may beacquired from within the genus Spiroplasma. Int J Syst Bacteriol. 45(1):178–181. Carle P, et al. 2010. Partial chromosome sequence of Spiroplasma citri non-Spiroplasma donors (Lo et al. 2015). 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Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii

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Abstract

Genome reduction is a recurring theme of symbiont evolution. The genus Spiroplasma contains species that are mostly facultative insect symbionts. The typical genome sizes of those species within the Apis clade were estimated to be 1.0–1.4 Mb. Intriguingly, Spiroplasma clarkii was found to have a genome size that is>30% larger than the median of other species within the same clade. To investigate the molecular evolution events that led to the genome expansion of this bacterium, we determined its complete genome sequence and inferred the evolutionary origin of each protein-coding gene based on the phylogenetic distribution of homologs. Among the 1,346 annotated protein-coding genes, 641 were originated from within the Apis clade while 233 were putatively acquired from outside of the clade (including 91 high-confidence candidates). Additionally, 472 were specific to S. clarkii without homologs in the current database (i.e., the origins remained unknown). The acquisition of protein-coding genes, rather than mobile genetic elements, appeared to be a major contributing factor of genome expansion. Notably,>50% of the high- confidence acquired genes are related to carbohydrate transport and metabolism, suggesting that these acquired genes contributed to the expansion of both genome size and metabolic capability. The findings of this work provided an interesting case against the general evolutionary trend observed among symbiotic bacteria and further demonstrated the flexibility of Spiroplasma genomes. For future studies, investigation on the functional integration of these acquired genes, as well as the inference of their contribution to fitness could improve our knowledge of symbiont evolution. Key words: mollicutes, Spiroplasma, symbiont, comparative genomics, horizontal gene transfer (HGT). Introduction mutualists of insects, which have genome sizes in the The patterns of genome evolution among diverse symbi- range of 0.1–1.0 Mb (Moran and Bennett 2014). otic bacteria are characterized by a general trend of ge- The genus Spiroplasma within the class Mollicutes contains nome reduction (Moran and Plague 2004; Ochman and diverse species that are mostly facultative insect symbionts Davalos 2006; Toft and Andersson 2010; McCutcheon capable of horizontal transmission (Gasparich et al. 2004; and Moran 2012; Moran and Bennett 2014). This obser- Regassa and Gasparich 2006; Gasparich 2010). In recent vation is likely a combined result of the mutational bias years, these bacteria have been developed into a model sys- towards deletions commonly observed in bacteria (Mira tem for the study of symbionts (Anbutsu and Fukatsu 2011; et al. 2001; Kuo and Ochman 2010), the lack of selection Bolanos et al. 2015; Lo et al. 2016). This paraphyletic genus against gene losses in stable and nutrient-rich environ- contains several major clades, with the Apis clade as the most ments, and the elevated levels of genetic drift due to genetically diverse and species-rich one. Based on the genome host restriction (Kuo et al. 2009; Novichkov et al. 2009). size estimates by pulsed-field gel electrophoresis (PFGE), most Although most free-living bacteria have a genome size of these Spiroplasma species haveagenomesizeof 1.0– that is>4 Mb, symbionts usually have a smaller genome. 1.4 Mb (Carle et al. 1995). Given these general observations, The most extreme examples of genome reduction were it is interesting to note that Spiroplasma clarkii, a facultative found among those obligate intracellular nutritional symbiont residing in the gut of larval/adult Scarabaeidae 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 1526 Genome Biol. Evol. 10(6):1526–1532. doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE beetles without apparent effect on its host, was found to have a genome size that is>30% larger than the median of other species within the same clade (Whitcomb et al. 1993). To investigate the evolutionary processes and the genetic changes that led to the genome expansion in this bacterium, we determined the complete genome sequence of S. clarkii for comparative analysis. Materials and Methods The procedures for genome sequencing and phylogenetic in- ference were based on those described in our previous studies (Lo,Chen, et al.2013; Lo, Ku, et al. 2013; Chang et al. 2014; Lo et al. 2015). The bioinformatics tools were used with the default settings unless stated otherwise. Briefly, the bacterial strain Spiroplasma clarkii CN-5 was acquired from the German Collection of Microorganisms and Cell Cultures (catalogue number: DSM 19994 ). For whole-genome shotgun sequenc- ing, one paired-end library (550 bp insert and 430X coverage) and one mate-pair library (4.5 kb insert and 60X coverage) were prepared and sequenced using the MiSeq platform (Illumina, USA). The de novo assembly was performed using ALLPATHS-LG release 52188 (Gnerre et al. 2011), followed by gap closure and validation using PCR and Sanger sequencing until the complete sequence of the circular chromosome was obtained. The programs RNAmmer (Lagesen et al. 2007), tRNAscan-SE (Lowe and Eddy 1997)and PRODIGAL (Hyatt et al. 2010) were used for gene prediction. The annotation was based on the homologous genes in other Spiroplasma genomes (supplementary table S1, Supplementary Material on- line) as identified by OrthoMCL (Li et al. 2003), followed by manual curation based on the KEGG (Kanehisa et al. 2016) and COG databases (Tatusov et al. 2003). To identify the homologs of protein-coding genes in other bacteria for each Apis clade species, we performed BLASTP (Camacho et al. 2009) search against the NCBI nonredundant database (version date: March 26, 2018). After removing the self-hit and low-quality hits (i.e., high-scoring pairs accounting for<90% of the query length or amino acid sequence sim- ilarity<40%), uptofive tophits were collected for eachquery (supplementary table S2, Supplementary Material online). Representative species from these hits (supplementary table S1, Supplementary Material online) were selected for an addi- tional round of homologous gene identification by OrthoMCL. Putatively acquired islands, defined as regions that have at least FIG.1.—Continued FIG.1.—Maximum likelihood phylogenies of representative lineages. species identified in the homologous gene search. The bootstrap support (A) A phylogram of the Apis clade based on a concatenated alignment of for each major clade is labeled above the branch; internal branches with a 412 single-copy genes and 148,728 aligned amino acid sites. All nodes bootstrap support below 80% were collapsed. Species highlighted with received>95% bootstrap support. The numbers in parentheses indicate “*” are those with genome sequences available and included in the iden- the chromosome size (unit: Mb) and the number of protein-coding genes. tification of horizontally transferred gene islands. All accession numbers (B) A cladogram based on the 16S rDNA phylogeny of the representative are provided in supplementary table S1, Supplementary Material online. Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 1527 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Tsai et al. GBE FIG.2.—Chromosomal organization of S. clarkii. Concentric circles from the inside out: 1) GC content (above average: dark gray; below average: light gray; two high GC peaks near the 0.5 Mb mark correspond to the rRNA gene clusters), 2) GC skew (positive: dark gray; negative: light gray), 3) locations of the high-confidence candidates of acquired genes (colored in red; putatively acquired islands with at least five genes from the same donor are highlighted with a pink background), 4–8) phylogenetic affiliations of the top five BLASTP hits from the NCBI nonredundant database (color-coded according to the legend), and 9) scale marks (unit: Mb). five acquired genes and exhibit synteny conservation with spe- species among all hits and processed using the same procedure. cies outside of the Apis clade, were identified. For the inference of individual gene trees, we relaxed the criteria For maximum likelihood phylogenetic analysis, two species for filtering out low quality BLASTP hits (i.e., high-scoring pairs phylogenies were inferred. The first one was focused on the accounting for<80% of the query length or amino acid se- Apis clade, the amino acid sequences of the shared single-copy quence similarity<30%) in an attempt to identify more distant genes were extracted from the OrthoMCL results used for an- homologs. Putatively acquired genes in S. clarkii with at least notation. The multiple sequence alignment was performed us- five homologs from other Apis clade species among the top 100 ing MUSCLE v3.8 (Edgar 2004) for each gene. The hits were selected for phylogenetic analysis using the same pro- concatenated alignment was analyzed using PhyML v3.0 cedure. The GenBank accession numbers for all of the sequen- (Guindon and Gascuel 2003). The proportion of invariable sites ces included in the phylogenetic analysis are provided in and the gamma distribution parameter were estimated from supplementary table S1, Supplementary Material online. the data set, the number of substitute rate categories was set to four. The bootstrap supports were estimated based on 1,000 Results and Discussion replicates. The second species phylogeny with broader taxon The complete genome sequence of S. clarkii contains one sampling was based on the BLASTP search result. The 16S circular chromosome that is 1.56 Mb in size; no plasmid rDNA sequences were extracted from the representative 1528 Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE Table 1 Classification of Protein-Coding Genes by Putative Origins Genome Apis Species-Specific HGT-Low Confidence HGT-High Confidence S. clarkii 641 (48%) 472 (35%) 142 (11%) 91 (7%) S. helicoides 679 (68%) 198 (20%) 99 (10%) 21 (2%) S. culicicola 709(66%) 228 (21%) 98(9%) 36(3%) S. apis 728 (63%) 281 (24%) 109 (10%) 33 (3%) S. turonicum 780 (73%) 149 (14%) 115 (11%) 20 (2%) S. corruscae 667(69%) 218 (22%) 70(7%) 18(2%) S. litorale 789 (74%) 151 (14%) 105 (10%) 21 (2%) S. cantharicola 745 (73%) 123 (12%) 104 (10%) 45 (4%) S. diminutum 770 (76%) 119 (12%) 115 (11%) 4 (0%) S. taiwanense 728 (85%) 50 (6%) 67 (8%) 13 (2%) S. sabaudiense 243 (26%) 338 (37%) 178 (19%) 165 (18%) NOTE.—Values indicate the gene count; the percentage of total is provided in parentheses. Due to the high level of sequence divergence from other Apis clade species, as well as its basal placement in the species phylogeny, this approach of utilizing BLASTP searches to classify the putative origin of genes is not applicable to S. sabaudiense. These values are provided for reference only and are not included in the calculation of average percentages among Apis clade species as discussed in the main text. was found. Although this size is 12% smaller than the group based on the same procedure and on average those 1.77 Mb estimate based on PFGE (Whitcomb et al. 1993), it species-specific genes account for only 16% of the total is still>30% larger than the median of other Apis clade spe- gene count in other Apis clade species. Unfortunately, al- cies with complete genome sequences available (fig. 1A). though the hypothesis that most of these species-specific Moreover, comparison between the actual genome size of genes were acquired through HGT is plausible, direct evidence these species with previous estimates (Carle et al. 1995; for or against this hypothesis is lacking. The remaining genes Williamson et al. 1996; Whitcomb et al. 1997; Helias et al. were assigned to two classes of HGT candidates, including 1998) revealed that the PFGE method typically overestimates 142 low-confidence ones (i.e., the top five hits involved a thegenomesize by 10–15%. mixture of species from within the Apis clade and other Examination of the chromosome organization and gene more divergent ones; 11% of the count and 9% of the content (fig. 2) revealed that the genome expansion was length) and 91 high-confidence ones (i.e., the top five hits not attributed to the invasion of plectroviruses as those found did not involve any Apis clade species; 7% of the count and within the Spiroplasma Citri clade, in which viral sequences 6% of the length). The low confidence candidates may in- account for 20% of the chromosome in extant species clude those acquired prior to the divergence between S. clarkii (Carle et al. 2010; Alexeev et al. 2012; Ku et al. 2013; Lo, and Spiroplasma helicoides, or those with more complex his- Chen, et al. 2013; Paredes et al. 2015). Rather, acquisition of tory such as multiple gain/loss events. However, due to the protein-coding genes through horizontal gene transfer (HGT) limited number of homologs available in the current database, appeared to be a major factor. Among the 1,346 annotated as well as the finding that many of these low confidence protein-coding genes, 641 (48% of the gene count and 45% candidates correspond to short hypothetical proteins, it is dif- of the chromosome length) were inferred as being originated ficult to infer the exact evolutionary history of these genes. from within the Apis clade (table 1). For these genes, the top Furthermore, because those low confidence candidates ac- five BLASTP hits within the NCBI nonredundant database did count for 10% of total gene count in other Apis clade spe- not involve any organism outside of the Apis clade, which cies as well, these genes are unlikely to be a main contributing suggested that these genes were either inherited vertically factor of genome expansion in S. clarkii. or at least did not involve recent HGT from donors outside Compared with other Apis clade species, the number and of the Apis clade. There are 472 species-specific genes (i.e., proportion of high-confidence HGT candidates are both those without any identifiable homolog in the current data- much higher in S. clarkii (table 1). This finding further sug- base), which correspond to 35% of the gene count and 29% gested that gene acquisition is a major contributing factor of of the chromosome length. These species-specific genes ap- the genome expansion. Among those 91 high-confidence pear to be the main contributing factor of the genome ex- candidates, 38% were inferred as originated from the sister pansion observed in S. clarkii (table 1). Although some of Mycoides-Entomoplasmataceae clade based on the phyloge- these may be artifacts of gene prediction, we expect that a netic distribution of homologs, whereas those from the Citri- high proportion of these genes may be acquired genes with- Chrysopicola-Mirum clade and other more divergent lineages out known donors. The reason for this inference is that all of within the class Mollicutes account for 13% and 17%, re- these Spiroplasma genomes were annotated by our research spectively (figs. 1B and 3A). Using individual gene phylogenies Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 1529 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Tsai et al. GBE FIG.3.—Classification of the high-confidence candidates of acquired genes. (A) Phylogenetic assignments of the most likely donors. (B) Functional assignments according to the COG categories. FIG.4.—Carbohydrate transport and metabolism. Genes that are putatively involved in horizontal transfer are highlighted by “*” (low-confidence) or “**” (high-confidence; color-coded according to the putative donors). For multicopy genes, subscripts following the gene name are used to distinguish different copies. Abbreviations: DHAP, dihydroxyacetone phosphate; G3P, glycerol-3-phosphate; GlcNAc, N-Acetylglucosamine; MDHA, monodehydroas- corbate; MurNAc, N-acetylmuramic acid. for the test of HGT hypothesis was not feasible for most of homologs in other Apis clade species, we inferred the individ- these candidates; 61 out of these 91 candidates did not have ual gene trees to investigate their evolutionary history (sup- any identifiable homolog in other Apis clade species. plementary fig. S1, Supplementary Material online). At least Although multiple independent losses in all other Apis clade four of these gene trees provided strong support for the HGT lineages may also explain the pattern and argue for vertical hypothesis. inheritance, such alternative hypothesis is less parsimonious Because the vast majority of Entomoplasmataceae/ compared with HGT. For the nine candidates with at least five Spiroplasmataceae species are affiliated with insect hosts for 1530 Genome Biol. Evol. 10(6):1526–1532 doi:10.1093/gbe/evy113 Advance Access publication June 1, 2018 Downloaded from https://academic.oup.com/gbe/article-abstract/10/6/1526/5026592 by Ed 'DeepDyve' Gillespie user on 20 June 2018 Genome Expansion in Spiroplasma clarkii GBE at leastapartoftheir life cycle (Gasparich et al. 2004; Regassa Acknowledgments and Gasparich 2006; Gasparich 2010; Gasparich 2014), this This work was supported by research grants from the Institute overlap in ecological niche could have promoted the HGT of Plant and Microbial Biology at Academia Sinica and the events among these lineages. Moreover, despite the phyloge- Ministry of Science and Technology of Taiwan [NSC 101- netic divergence, all these Mollicutes lineages share the same 2621-B-001-004-MY3 and MOST 104-2311-B-001-019] to alternative genetic code (i.e., UGA changed from stop to tryp- C.H.K. The funders had no role in study design, data collection tophan) and a strong nucleotide composition bias toward and interpretation, or the decision to submit the work for Aþ T. These shared genomic traits could have promoted publication. The bacterial strain was imported under the per- the retention and integration of those acquired genes (Lo mit number 103-B-001 (Council of Agriculture, Taiwan). The and Kuo 2017). The chromosomal region at 0.9–1.1 Mb Sanger sequencing service and the Illumina sequencing library appeared to be the major hot spot for foreign genes preparation service were provided by the Genomic (fig. 2). A total of 45 genes were identified in seven islands Technology Core Facility (Institute of Plant and Microbial with at least five acquired genes from the same donor with Biology, Academia Sinica). The Illumina MiSeq sequencing synteny conservation. Interestingly, most of the gene acquis- service was provided by the Genomics Core Facility (Institute itions did not disrupt the patterns of GC skew and gene ori- of Molecular Biology, Academia Sinica). We thank Dr. Wen- entation (fig. 2), suggesting that those that did may be Sui Lo for technical assistance. selected against. Regarding the functions, carbohydrate transport and me- tabolism is the most dominant category that accounts for Literature Cited 51% of those high-confidence candidates (fig. 3B). This find- Alexeev D, et al. 2012. Application of Spiroplasma melliferum proteoge- nomic profiling for the discovery of virulence factors and pathogenicity ing is worth noting because carbohydrate metabolism is mechanisms in host-associated spiroplasmas. J Proteome Res. highly variable among Spiroplasma species (Chang et al. 11(1):224–236. 2014; Lo et al. 2015) and is important in their physiology Anbutsu H, Fukatsu T. 2011. 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