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Plastid genome degradation in the endangered, mycoheterotrophic, North American orchid Hexalectris warnockii

Plastid genome degradation in the endangered, mycoheterotrophic, North American orchid... Genome Report: plastid genome degradation in the endangered Hexalectris warnockii PLASTID GENOME DEGRADATION IN THE ENDANGERED, MYCOHETEROTROPHIC, NORTH AMERICAN ORCHID HEXALECTRIS WARNOCKII. 1* 2 Craig F. Barrett , Aaron H. Kennedy . Department of Biology, 53 Campus Drive, West Virginia, University, Morgantown, WV USA Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Bldg 010a, 10300 Baltimore Blvd., Beltsville, MD USA 20705. *Author for correspondence. Craig F. Barrett, Department of Biology, West Virginia University, Morgantown, West Virginia, USA phone: (304) 293-7506, e-mail address: cfb0001@mail.wvu.edu, phone: (304) 293-7506. Keywords: orchid, heterotroph, plastome, pseudogene, evolution, chloroplast © 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 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii ABSTRACT Heterotrophic plants provide evolutionarily independent, natural experiments in the genomic consequences of radically altered nutritional regimes. Here we have sequenced and annotated the plastid genome of the endangered mycoheterotrophic orchid Hexalectris warnockii. This orchid bears a plastid genome that is ~80% the total length of the leafy, photosynthetic Phalaenopsis, and contains just over half the number of putatively functional genes of the latter. The plastid genome of H. warnockii bears pseudogenes and has experienced losses of genes encoding proteins directly (e.g. psa/psb, rbcL) and indirectly involved in photosynthesis (atp genes), suggesting it has progressed beyond the initial stages of plastome degradation, based on previous models of plastid genome evolution. Several dispersed and tandem repeats were detected, that are potentially useful as conservation genetic markers. Also, a 29 kb inversion and a significant contraction of the inverted repeat boundaries are observed in this plastome. The Hexalectris warnockii plastid genome adds to a growing body of data useful in refining evolutionary models in parasites, and provides a resource for conservation studies in these endangered orchids. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii INTRODUCTION Plants that parasitize other plants or mycorrhizal fungi provide unique opportunities to study the genomic consequences of radically altered nutritional lifestyles and associated changes in selective regimes (e.g. Wolfe et al., 1992; Barrett et al., 2014; Wicke et al., 2016). In particular, plants that have become obligate parasites upon fungi for nutritional needs represent case studies of convergent evolution. Transitions to this lifestyle have occurred an estimated minimum of 30× in the orchid family alone, mostly due to their complete, parasitic dependence upon mycorrhizal fungi early in development, called ‘initial mycoheterotrophy’ (Freudenstein and Barrett, 2008; Merckx and Freudenstein, 2010). Furthermore, many of these plants are rare or endangered (e.g. Freudenstein, 1999; Merckx et al., 2013), and in many cases represent ‘ecological indicators’ of undisturbed habitat, or may serve as ‘umbrella species’ for conservation efforts (e.g. Taylor et al., 2013). What happens to the genomes of organisms that have undergone such drastic changes in nutritional mode, from autotrophy to heterotrophy? Representative plastid genomes have been sequenced from plant lineages containing heterotrophs, allowing researchers to construct models of plastid genome degradation, including pseudogene formation (functional losses), physical gene losses, and increased substitution rates as a result of relaxed selective pressures on photosynthetic function (e.g. Wicke et al., 2011; Barrett & Davis, 2012; Barrett et al., 2014; Wicke et al, 2016; Graham et al., 2017). However, sampling gaps exist in these models, underscoring the need for more thorough representation of plant lineages containing non- photosynthetic members, each representing an independent trajectory of plastome degradation. One such lineage is the North American orchid genus Hexalectris Raf. Members of this genus are hypothesized to obtain most or all nutrients, including carbon, from their symbiotic Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii mycorrhizal fungi (Taylor et al., 2003; Kennedy et al., 2011), a situation called mycoheterotrophy. Hexalectris contains ten currently recognized species, many of which are rare and restricted to highly specific habitats (Catling and Engle, 1993; Catling, 2004; Kennedy and Watson, 2010). Hexalectris warnockii Ames and Correll, or the Texas purple-spike, is an endangered member of the genus restricted to Texas, Arizona, and Mexico, where it grows in shaded oak-juniper-pinyon canyons near seasonally dry creek beds, or on calcareous soils under juniper scrub (IUCN Red List: Endangered D; Goedeke et al., 2015). It is known from approximately 24 sites in the USA, including: Big Bend National Park, northeastern Texas (Dallas area), the Edwards Plateau, and Arizona; in Mexico it is found at a site in Coahuila and another at the southern tip of Baja California Sur (Catling, 2004). Here we have sequenced, assembled, and annotated the plastid genome of Hexalectris warnockii. The goals of this study are: 1) to use genomic criteria—i.e. extensive loss of photosynthesis-related genes—to determine if H. warnockii is non-photosynthetic (fully mycoheterotrophic) or retains photosynthetic capability (partially mycoheterotrophic); 2) to compare the plastid genome of H. warnockii to those from members of other heterotrophic plant lineages; and 3) to provide a genomic resource for the development of plastid markers to facilitate studies of genetic diversity in populations of this endangered species. MATERIALS AND METHODS Floral tissue of H. warnockii was collected from Brewster County, Texas, USA. A voucher specimen was deposited at The Miami University Willard Sherman Turrell Herbarium (Accession: Kennedy and Freeman #33). We extracted DNA using a CTAB protocol (Doyle and Doyle, 1987), yielding 17.4 ng/ul based on a Qubit Fluorometer reading (ThermoFisher Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Scientific, Waltham, Massachusetts, USA). Illumina libraries were prepared by shearing total genomic DNA to 350-400 bp fragments on a Covaris E220 ultrasonicator (Covaris, Woburn, Massachusetts, USA), followed by the protocol of Glenn et al. (2016). Library concentrations and fragment sizes were calculated on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California, USA), pooled with 19 other libraries, and sequenced on two lanes of an Illumina Hiseq2000 for paired-end, 100 bp reads. We carried out adapter removal and quality trimming with Trimmomatic v.0.36 (Bolger et al., 2014), using a 3-bp sliding window and a minimum PHRED score of 20 (1:100 error rate). The plastome was assembled from cleaned reads using NOVOPlasty v.2.6.3 (Diercksens et al., 2016), which uses a reference sequence as an initial seed (here, rbcL from the leafy, photosynthetic orchid Phalaenopsis equestris, GenBank# JF719062) and builds a circularized plastome. Reads were mapped with high stringency to the draft plastome produced by NOVOplasty in Geneious v.8.1 to check for assembly errors (http://www.geneious.com, Kearse et al., 2012; 98% similarity, allowing gaps up to 100 bp). The plastome was annotated initially in DOGMA (Wyman et al, 2004). Start/stop codons, exon/intron boundaries, inverted repeat (IR) boundaries, and putative loss-of-function pseudogenes were verified and adjusted by aligning the plastome to protein coding and RNA genes from P. equestris (GenBank accession JF719062), Phoenix dactylifera (Arecaceae, GU811709), and Heliconia collinsiana (Heliconiaceae, JX08866), as was done in Barrett et al. (2014) The annotated H. warnockii plastome was aligned with that of P. equestris using the progressiveMAUVE (Darling et al., 2010) plugin for Geneious v. 8.1, which identifies syntenic regions between two or more genomes, thus allowing detection of genomic rearrangements. Putatively functional genes (with open reading frames or lacking drastic modifications in the Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii case of RNA genes), pseudogenes (putative functional losses, i.e. those with interrupted reading frames or non-triplet insertions or deletions), and physical gene losses were recorded and compared with the plastome of the leafy, photosynthetic P. equestris. We also compared plastome size and functional gene content for a number of full mycoheterotrophs, partial mycoheterotrophs, holoparasites, hemiparasites, and other leafy, autotrophic species. Genomic repeat type and abundance were calculated in REPuter (Kurtz et al., 2001), specifying a minimum length of 20 bp (for forward, reverse, palindromic, and reverse- -3 complementary repeats), a Hamming distance of 3, and a maximum e-value of 1.0 × 10 . Tandem repeats were identified using the Phobos plugin for Geneious (Mayer et al., 2010), specifying 2-50 bp motif length, a minimum total length of 10 bp, and allowing only perfect repeats. All results were plotted in R (R Core Development Team) or PAST v.3.8 (Hammer et al., 2001). A linearized plastome map was created in OGDraw (Lohse et al., 2013). The annotated H. warnockii plastome is deposited under NCBI accession XXXXXXXX. RESULTS AND DISCUSSION Illumina paired-end sequencing of H. warnockii yielded a total of 38,633,900 reads (after trimming), with an average insert size of 350 bp. Coverage depth of the finished plastome was 712.2×, representing 2.19% of the total read pool. The 119,057 bp plastome has a quadripartite structure as is typical for angiosperms (Fig. 1), with a Large Single Copy region (LSC; 66,903 bp), Small Single Copy region (SSC; 17,490), and an Inverted Repeat (IR; 17,332) (Table 1; Fig. 1). The H. warnockii plastome is thus 29,902 bp smaller than the leafy orchid P. equestris, or approximately 79.9% the total size of the latter (148,959 bp, representing a typical orchid plastome size). The largest physical reduction in the H. warnockii plastome was in the LSC Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii region, which was 27.6% smaller than that of P. equestris due to several large deletions. There is a contraction of the inverted repeat (IR) in H. warnockii, representing a 33% difference in total IR length relative to P. equestris. This contraction resulted in the following genes, typically GAU UGC found in the IR, becoming part of the SSC: 16S rRNA, trnI , trnA , 23S rRNA, 4.5S rRNA, ACG GUU 5S rRNA, trnR , trnN , and the 5’ portion of ycf1. Total GC content is 36.9% after removing one copy of the IR, and similar to that of Phalaenopsis at 36.7%. We identified 45 dispersed repeats across the genome passing our filters in REPuter: two were forward-compliment, 16 forward-forward, 22 palindromic, and five forward-reverse (Table 2). We identified 419 tandem repeats with minimum motif lengths of 10 bp (Table 2; Table S1). The most abundant of these were hexanucleotide repeats (141) followed by pentanucleotide repeats (99). We identified three dinucleotide repeats, 17 trinucleotide repeats, and 50 tetranucleotide repeats. Thus, there are several options for the development of potentially variable satellite markers in H. warnocki, which will be useful in determining patterns of plastid genomic diversity across populations of this endangered orchid. Alignment with MAUVE detected a major genomic inversion of a ~29 kb region of the LSC relative to P. equestris with GCU GGA breakpoints spanning trnS and trnS ; the entire collinear block detected by MAUVE contains 29 genes (Fig. 1). The plastome of H. warnockii encodes 72 putatively functional genes (protein-coding, tRNA, and rRNA), compared to 103 in P. equestris, a 31.1% difference in functional gene content, composed of pseudogenes (i.e. functional losses, 25 in H. warnockii relative to P. equestris) and physical gene losses (11 in H. warnockii relative to P. equestris). The total plastome size reduction in H. warnockii is largely due to the deletion of regions containing photosynthesis-related genes (Fig. 1), thus also reducing the gene count. Plastome size in H. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii warnockii is comparable to that of the mycoheterotrophic orchid Corallorhiza striata var. vreelandii at 137,505 bp (Barrett and Davis, 2012), and to the holoparasite Myzorhiza californica at 120,840 bp (Wicke et al., 2013; see Fig. 2). Overall there is a strong positive correlation between the number of putatively functional genes and plastome length among heterotrophic angiosperms (Fig. 2; Pearson correlation r = 0.953, p < 0.0001); thus, physical gene loss is at least in part driving a reduction in plastome size. Genes that are either functionally or physically lost conform to the models of Barrett and Davis (2012), Wicke et al. (2016) and Graham et al. (2017), and include: photosynthesis-related genes [Photosystem I and I subunits (psa, psb), Cytochrome subunits (pet), RuBisCO Large Subunit (rbcL), Photosystem Assembly Factors (ycf3, ycf4, also called paf1 and paf2 respectively; Wicke et al., 2011); subunits of the plastid-encoded RNA Polymerase (rpo); and subunits of the ATP synthase complex (atp). There are also substantial functional and physical losses among subunits of the NAD(P)H Dehydrogenase complex (ndh; all physically lost except ndhK, ψndhB, and ψndhC), but this is common in other orchids including Phalaenopsis, perhaps due to the tendency of orchids to occupy low-light environments (e.g. Lin et al., 2017). Losses in subunits of these functional gene categories conform to ‘stage 4’ of the model of plastome degradation by Barrett and Davis (2012), and are also in line with a recent mechanistic model of plastome evolution (Wicke et al. 2016). Functional loss of five out of six ATP Synthase subunit genes is significant, in that many parasitic lineages early in the process of plastome degradation tend to have preserved reading frames for atp genes despite having experienced major losses in photosynthesis-related and rpo genes (Barrett et al., 2014; Wicke et al., 2016; Braukmann et al., 2017; Graham et al., 2017). Thus, H. warnockii may have entered a Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii new phase in plastome evolution following a period of evolutionary stasis, based on the ‘punctuated burst’ model of plastome evolution put forth by Naumann et al. (2016). The IR is hypothesized to function in plastid genome structural stability, but studies from highly rearranged genomes are equivocal (Palmer, 1995; Lam et al. 2015; Lim et al., 2015). Here, a 29 kb LSC inversion is found in conjunction with a drastic reduction of the IR (Fig. 1). Repeats have been shown in parasitic Orobanchaceae to be associated with plastome structural rearrangements and shifts in IR boundaries (Wicke et al. 2013); thus additional sampling of Hexalectris spp. and related genera will allow for explicit tests among repeat content, structural rearrangements, and substitution rates. The ancestor of Hexalectris may have been evolving under relaxed selective pressure for up to 32 million years, based on a stem-node age estimate of Hexalectris, which also includes members of the closely related genera Basiphyllaea and Bletia (Sosa et al., 2016). Hexalectris warnockii is consistently placed as sister to the remaining members of genus Hexalectris in previous studies (Kennedy and Watson, 2010; Sosa et al., 2016); thus it is unknown whether this species has undergone an independent transition to full mycoheterotrophy, or if this condition is shared by all species in the genus. Regardless, plastome degradation has been occurring in H. warnockii for an estimated 24 million years, when the first divergence occurred within Hexalectris (Sosa et al., 2016). Sequencing of additional members of Hexalectris, and the closely related members of tribe Bletiinae (Basiphyllaea, Bletia) will allow fine-scale reconstruction of plastid genome degradation, and testing of the hypothesis of a single origin of full mycoheterotrophy/loss of photosynthesis in Hexalectris. Furthermore, sampling of multiple individuals per species may uncover substantial variation in plastomes across the geographic Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii range of each species, as has been recently demonstrated in the fully mycoheterotrophic orchid Corallorhiza striata (Barrett et al., 2018). ACKNOWLEDGEMENTS We thank Big Bend National Park (US Department of Interior) for permission and assistance in collecting material; this research was supported by the West Virginia University Program to Stimulate Competitive Research Grant to CB. We thank two anonymous reviewers for suggestions that improved the manuscript. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii LITERATURE CITED Barrett CF, Davis JI. 2012. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. American Journal of Botany 99: 1513-1523. Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, et al. 2014. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution 31: 3095-3112. Barrett CF, Wicke S, Sass C. 2018. Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex. New Phytologist, in press. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. Braukmann TWA, Broe MB, Stefanović S, Freudenstein JV. 2017. On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae. New Phytologist 216: 254-266. Catling, P.M. 2004. A synopsis of the genus Hexalectris in the United States and a new variety of Hexalectris revoluta. The Native Orchid Conference Journal 1: 5-25. Catling, P. M. and V. S. Engel. 1993. Systematics and distribution of Hexalectris spicata var. arizonica (Orchidaceae). Lindleyana 8: 119–125. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147. https://doi.org/10.1371/journal.pone.0011147. Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii genomes from whole genome data. Nucleic Acids Research 45: e18. https://doi:10.1093/nar/gkw955. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15. Freudenstein JV. 1999. A new species of Corallorhiza (Orchidaceae) from West Virginia, USA. Novon 9: 511-513. Freudenstein JV, Barrett CF. 2010. Mycoheterotrophy and diversity in Orchidaceae. In: Seberg O, Petersen G, Barfod A, Davis JI, editors. Diversity, phylogeny and evolution in the monocotyledons. The Proceedings of the Fourth International Conference on Monocot Systematics. Aarhus (Denmark): Aarhus University Press. p. 25-37. Glenn TC, Nilsen R, Kieran TJ, Finger JW, Pierson TW, et al. 2016. Adapterama I: Universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru &amp; iNext). BioRxiv 049114. https://doi.org/10.1101/049114. Goedeke, T., Sharma, J., Treher, A., Frances, A. & Poff, K. 2015. Hexalectris warnockii. The IUCN Red List of Threatened Species 2015: http://dx.doi.org/10.2305/IUCN.UK.2015-4.RLTS.T64176203A64176207.en. Graham SW, Lam VK, Merckx VS. 2017. Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes. New Phytologist 214: 48-55. Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4: 1-9. Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772-780. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649. Kennedy AH, Taylor DL, Watson LE. 2011. Mycorrhizal specificity in the fully mycoheterotrophic Hexalectris Raf. (Orchidaceae: Epidendroideae). Molecular Ecology 20: 1303-1316. Kennedy AH, Watson LE. 2010. Species delimitations and phylogenetic relationships within the fully myco-heterotrophic Hexalectris (Orchidaceae). Systematic Botany 35: 64- Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29: 4633-4642. Lam VK, Soto Gomez M, Graham SW. 2015. The highly reduced plastome of mycoheterotrophic Sciaphila (Triuridaceae) is colinear with its green relatives and is under strong purifying selection. Genome Biology and Evolution 7: 2220-2236. Lim GS, Barrett CF, Pang CC, Davis JI. 2016. Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri. American Journal of Botany 103: 1129-1137. Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, et al. 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant Journal 90: 994- Lohse M, Drechsel O, Kahlau S, Bock R. 2013. OrganellarGenomeDRAW-a suite of tools Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41: W575-W581. Mayer C. 2010. Phobos 3.3.11. http://www.rub.de/ecoevo/cm/cm_phobos.htm. Merckx V, Freudenstein JV. 2010. Evolution of mycoheterotrophy in plants: a phylogenetic perspective. New Phytologist 185: 605-609. Merckx VSFT, Smets EF, Specht CD. 2013. Biogeography and conservation of mycoheterotrophic plants. Merckx V, editor. Mycoheterotrophy: The Biology of Plants Living on Fungi. New York: Springer. p. 103-156. Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, et al. 2016. Detecting and characterizing the highly divergent plastid genome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae). Genome Biology and Evolution 8: 345-363. Palmer JD. 1985. Comparative organization of chloroplast genomes. Annual Review of Genetics 19: 325-354. R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/. Sosa V, Cameron KM, Angulo DF, Hernandez-Hernandez T. 2016. Life form evolution in epidendroid orchids: Ecological consequences of the shift from epiphytism to terrestrial habit in Hexalectris. Taxon 65: 235-248. Taylor DL, Bruns TD, Szaro TM, Hodges SA. 2003. Divergence in mycorrhizal specialization within Hexalectris spicata (Orchidaceae), a nonphotosynthetic desert orchid. American Journal of Botany 90: 1168-1179. Taylor DL, Barrett C, Beatty G, Kennedy A, Klooster M, et al. 2013. Progress and prospects for the ecological genetics of mycoheterotrophs. pp 245-266 In Mycoheterotrophy: Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii The Biology of Plants Living on Fungi. Merckx V, editor. New York: Springer. p. 245-266. Wicke S, Schneeweiss GM, dePamphilis CW, Muller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology 76: 273-297. Wicke S, Muller KF, de Pamphilis CW, Quandt D, Wickett NJ, et al. 2013. Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. Plant Cell 25: 3711-3725. Wicke S, Muller KF, dePamphilis CW, Quandt D, Bellot S, et al. 2016. Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences of the United States of America 113: 9045-9050. Wolfe KH, Morden CW, Palmer JD. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences of the United States of America 89: 10648-10652. Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Table 1. Features of the fully mycoheterotrophic Hexalectris warnockii plastid genome relative to that of the leafy, autotrophic Phalaenopsis equestris (GenBank accession JF719062). Hexalectris Phalaenopsis % of warnockii equestris Phalaenopsis Total Length (bp) 119,057 148,959 79.9 Large single copy (LSC) 66,903 85,967 77.8 Inverted repeat (IR) 17,332 25,846 67.1 Small single copy (SSC) 17,490 11,300 154.8 protein coding genes (CDS) 38 69 55.1 Pseudogenes (ψ) 25 3 833.3 Transfer RNA genes (tRNA) 30 30 93.3 Ribosomal RNA genes (rRNA) 4 4 100.0 Putatively functional 72 103 69.9 Total genes & pseudogenes 97 106 91.5 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Table 2. Numbers of dispersed and tandem repeats detected with REPuter and Phobos, respectively. Tandem repeat sequences are listed in Table S1. Dispersed repeats Repeat type number forward-compliment 2 forward-forward 16 palindromic 22 forward-reverse 5 Tandem repeats Motif length (bp) number 2 3 3 17 4 50 5 99 6 141 7 50 8 19 9 15 >9 25 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii FIGURE LEGENDS Fig. 1. Map of the plastid genome of Hexalectris warnockii. ‘LSC’ = large single copy region; ‘SSC’ = small single copy region; gray = inverted repeat; dashed line in LSC = a 29 kb inversion. Red text indicates the presence of a pseudogene (ψ). ‘*’ and “**’ denote genes with one or two introns, respectively. Fig. 2. A comparison of plastid genome size and the number of putatively functional genes for sequenced holoparasites (gray), full mycoheterotrophs (black), and selected autotrophs (including partial mycoheterotrophs and hemiparasites; green), with trophic status based on whether or not photosynthetic genes are putatively functional in each. Inset: Hexalectris warnockii in flower (photo: A. Kennedy; Big Bend National Park, Brewster Co., TX, USA). Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 photosystem I RubisCO large subunit ycf genes Hexalectris warnockii photosystem II RNA polymerase ORFs cytochrome b/f complex ribosomal proteins (SSU) transfer RNAs chloroplast genome 10kb ATP synthase ribosomal proteins (LSU) ribosomal RNAs NADH dehydrogenase accD, clpP, matK (ψ) = pseudogene 119,057 bp *, ** = intron(s) LSC Inverted Repeat A ycf2 ycf1 ycf2 Inverted SSC Repeat B Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 psbA(ψ) mat K trnK-UUU rps16* trnQ-UUG psbK(ψ) trnS-GCU ycf3 (ψ) psaA(ψ) psaB(ψ) rps1 4 trnG-UCC trnfM-CAU trnS-CGA psbZ psbC(ψ) psbD(ψ) trnT-GGU trnE-UUC trnY-GUA trnD-GUC petN(ψ) psbM trnC-GCA rpoC1(ψ) rpoC2(ψ) rps2 atpI(ψ) atpH atpF(ψ) atpA(ψ) trnR-UCU trnG-UCC* trnS-GCU rps4 trnL-UAA* trnT-UGU ndhK ndhC(ψ) trnF-GAA trnV-UAC* trnM-CAU atpE(ψ) rbcL(ψ) atpB(ψ) accD psaI ycf4(ψ) cemA(ψ) psbJ petA(ψ) psbL pet L psbF psbE pet G trnW-CCA rpl3 3 trnP-UGG rps18 rpl20 rps12(5’) clpP** psbB(ψ) rpoA(ψ) petD(ψ) rps11 rpl3 6 rps8 rpl14 rpl16 rps3 rpl22 trnH-GUG rps1 9 rpl2* rpl23 trnI-CAU trnL-CAA ndhB(ψ) rps7 rps12_3end rpl3 2 trnL-UAG ccsA(ψ) trnV-GAC 16S rRNA trnI-GAU* trnA-UGC* 23S rRNA 4.5S rRNA 5S rRNA trnR-ACG trnN-GUU rpl32 (partial) rps15 rps12 (3’)* rps7 ndhB(ψ) trnL-GAG trnI-CAU rpl23 rpl2* trnH-GUG rps19 rpl22 rps3 Leafy, partially mycoheterotrophic, and hemiparasitic taxa Cuscuta exaltata Cuscuta reflexa Cuscuta obtusiflora Hexalectris Corallorhiza mertensiana Corallorhiza mac. maculata warnockii Cuscuta Corallorhiza Corallorhiza mac. occidentalis gronovii striata Lathraea squamaria Myzorrhiza californica Aphyllorchis montana Petrosavia stellaris Neottia camtschatea Neottia acuminata Phelipanche Neottia listeroides purpurea Orobanche crenata 60 Orobanche Cistanche phelypaea gracilis Neottia nidus-avis Phelipanche Conopholis ramosa Boulardia latisquama americana Epifagus Hypopitys virginiana monotropa Sciaphila Rhizanthella gardneri densiflora Epipogium Holoparasite roseum Epipogium aphyllum Full mycoheterotroph Cytinus hypocistis Hydnora visseri Leafy, partial mycoheterotroph, or hemiparasite Thismia tentaculata Pilostyles hamiltonii Pilostyles aethiopica 0 30000 60000 90000 120000 150000 160000 Length of plastome (bp) Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Number of putatively functional genes http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Genome Biology and Evolution Oxford University Press

Plastid genome degradation in the endangered, mycoheterotrophic, North American orchid Hexalectris warnockii

Barrett, Craig F; Kennedy, Aaron H
Genome Biology and Evolution , Volume Advance Article – May 29, 2018
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© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Abstract

Genome Report: plastid genome degradation in the endangered Hexalectris warnockii PLASTID GENOME DEGRADATION IN THE ENDANGERED, MYCOHETEROTROPHIC, NORTH AMERICAN ORCHID HEXALECTRIS WARNOCKII. 1* 2 Craig F. Barrett , Aaron H. Kennedy . Department of Biology, 53 Campus Drive, West Virginia, University, Morgantown, WV USA Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Bldg 010a, 10300 Baltimore Blvd., Beltsville, MD USA 20705. *Author for correspondence. Craig F. Barrett, Department of Biology, West Virginia University, Morgantown, West Virginia, USA phone: (304) 293-7506, e-mail address: cfb0001@mail.wvu.edu, phone: (304) 293-7506. Keywords: orchid, heterotroph, plastome, pseudogene, evolution, chloroplast © 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 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii ABSTRACT Heterotrophic plants provide evolutionarily independent, natural experiments in the genomic consequences of radically altered nutritional regimes. Here we have sequenced and annotated the plastid genome of the endangered mycoheterotrophic orchid Hexalectris warnockii. This orchid bears a plastid genome that is ~80% the total length of the leafy, photosynthetic Phalaenopsis, and contains just over half the number of putatively functional genes of the latter. The plastid genome of H. warnockii bears pseudogenes and has experienced losses of genes encoding proteins directly (e.g. psa/psb, rbcL) and indirectly involved in photosynthesis (atp genes), suggesting it has progressed beyond the initial stages of plastome degradation, based on previous models of plastid genome evolution. Several dispersed and tandem repeats were detected, that are potentially useful as conservation genetic markers. Also, a 29 kb inversion and a significant contraction of the inverted repeat boundaries are observed in this plastome. The Hexalectris warnockii plastid genome adds to a growing body of data useful in refining evolutionary models in parasites, and provides a resource for conservation studies in these endangered orchids. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii INTRODUCTION Plants that parasitize other plants or mycorrhizal fungi provide unique opportunities to study the genomic consequences of radically altered nutritional lifestyles and associated changes in selective regimes (e.g. Wolfe et al., 1992; Barrett et al., 2014; Wicke et al., 2016). In particular, plants that have become obligate parasites upon fungi for nutritional needs represent case studies of convergent evolution. Transitions to this lifestyle have occurred an estimated minimum of 30× in the orchid family alone, mostly due to their complete, parasitic dependence upon mycorrhizal fungi early in development, called ‘initial mycoheterotrophy’ (Freudenstein and Barrett, 2008; Merckx and Freudenstein, 2010). Furthermore, many of these plants are rare or endangered (e.g. Freudenstein, 1999; Merckx et al., 2013), and in many cases represent ‘ecological indicators’ of undisturbed habitat, or may serve as ‘umbrella species’ for conservation efforts (e.g. Taylor et al., 2013). What happens to the genomes of organisms that have undergone such drastic changes in nutritional mode, from autotrophy to heterotrophy? Representative plastid genomes have been sequenced from plant lineages containing heterotrophs, allowing researchers to construct models of plastid genome degradation, including pseudogene formation (functional losses), physical gene losses, and increased substitution rates as a result of relaxed selective pressures on photosynthetic function (e.g. Wicke et al., 2011; Barrett & Davis, 2012; Barrett et al., 2014; Wicke et al, 2016; Graham et al., 2017). However, sampling gaps exist in these models, underscoring the need for more thorough representation of plant lineages containing non- photosynthetic members, each representing an independent trajectory of plastome degradation. One such lineage is the North American orchid genus Hexalectris Raf. Members of this genus are hypothesized to obtain most or all nutrients, including carbon, from their symbiotic Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii mycorrhizal fungi (Taylor et al., 2003; Kennedy et al., 2011), a situation called mycoheterotrophy. Hexalectris contains ten currently recognized species, many of which are rare and restricted to highly specific habitats (Catling and Engle, 1993; Catling, 2004; Kennedy and Watson, 2010). Hexalectris warnockii Ames and Correll, or the Texas purple-spike, is an endangered member of the genus restricted to Texas, Arizona, and Mexico, where it grows in shaded oak-juniper-pinyon canyons near seasonally dry creek beds, or on calcareous soils under juniper scrub (IUCN Red List: Endangered D; Goedeke et al., 2015). It is known from approximately 24 sites in the USA, including: Big Bend National Park, northeastern Texas (Dallas area), the Edwards Plateau, and Arizona; in Mexico it is found at a site in Coahuila and another at the southern tip of Baja California Sur (Catling, 2004). Here we have sequenced, assembled, and annotated the plastid genome of Hexalectris warnockii. The goals of this study are: 1) to use genomic criteria—i.e. extensive loss of photosynthesis-related genes—to determine if H. warnockii is non-photosynthetic (fully mycoheterotrophic) or retains photosynthetic capability (partially mycoheterotrophic); 2) to compare the plastid genome of H. warnockii to those from members of other heterotrophic plant lineages; and 3) to provide a genomic resource for the development of plastid markers to facilitate studies of genetic diversity in populations of this endangered species. MATERIALS AND METHODS Floral tissue of H. warnockii was collected from Brewster County, Texas, USA. A voucher specimen was deposited at The Miami University Willard Sherman Turrell Herbarium (Accession: Kennedy and Freeman #33). We extracted DNA using a CTAB protocol (Doyle and Doyle, 1987), yielding 17.4 ng/ul based on a Qubit Fluorometer reading (ThermoFisher Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Scientific, Waltham, Massachusetts, USA). Illumina libraries were prepared by shearing total genomic DNA to 350-400 bp fragments on a Covaris E220 ultrasonicator (Covaris, Woburn, Massachusetts, USA), followed by the protocol of Glenn et al. (2016). Library concentrations and fragment sizes were calculated on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California, USA), pooled with 19 other libraries, and sequenced on two lanes of an Illumina Hiseq2000 for paired-end, 100 bp reads. We carried out adapter removal and quality trimming with Trimmomatic v.0.36 (Bolger et al., 2014), using a 3-bp sliding window and a minimum PHRED score of 20 (1:100 error rate). The plastome was assembled from cleaned reads using NOVOPlasty v.2.6.3 (Diercksens et al., 2016), which uses a reference sequence as an initial seed (here, rbcL from the leafy, photosynthetic orchid Phalaenopsis equestris, GenBank# JF719062) and builds a circularized plastome. Reads were mapped with high stringency to the draft plastome produced by NOVOplasty in Geneious v.8.1 to check for assembly errors (http://www.geneious.com, Kearse et al., 2012; 98% similarity, allowing gaps up to 100 bp). The plastome was annotated initially in DOGMA (Wyman et al, 2004). Start/stop codons, exon/intron boundaries, inverted repeat (IR) boundaries, and putative loss-of-function pseudogenes were verified and adjusted by aligning the plastome to protein coding and RNA genes from P. equestris (GenBank accession JF719062), Phoenix dactylifera (Arecaceae, GU811709), and Heliconia collinsiana (Heliconiaceae, JX08866), as was done in Barrett et al. (2014) The annotated H. warnockii plastome was aligned with that of P. equestris using the progressiveMAUVE (Darling et al., 2010) plugin for Geneious v. 8.1, which identifies syntenic regions between two or more genomes, thus allowing detection of genomic rearrangements. Putatively functional genes (with open reading frames or lacking drastic modifications in the Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii case of RNA genes), pseudogenes (putative functional losses, i.e. those with interrupted reading frames or non-triplet insertions or deletions), and physical gene losses were recorded and compared with the plastome of the leafy, photosynthetic P. equestris. We also compared plastome size and functional gene content for a number of full mycoheterotrophs, partial mycoheterotrophs, holoparasites, hemiparasites, and other leafy, autotrophic species. Genomic repeat type and abundance were calculated in REPuter (Kurtz et al., 2001), specifying a minimum length of 20 bp (for forward, reverse, palindromic, and reverse- -3 complementary repeats), a Hamming distance of 3, and a maximum e-value of 1.0 × 10 . Tandem repeats were identified using the Phobos plugin for Geneious (Mayer et al., 2010), specifying 2-50 bp motif length, a minimum total length of 10 bp, and allowing only perfect repeats. All results were plotted in R (R Core Development Team) or PAST v.3.8 (Hammer et al., 2001). A linearized plastome map was created in OGDraw (Lohse et al., 2013). The annotated H. warnockii plastome is deposited under NCBI accession XXXXXXXX. RESULTS AND DISCUSSION Illumina paired-end sequencing of H. warnockii yielded a total of 38,633,900 reads (after trimming), with an average insert size of 350 bp. Coverage depth of the finished plastome was 712.2×, representing 2.19% of the total read pool. The 119,057 bp plastome has a quadripartite structure as is typical for angiosperms (Fig. 1), with a Large Single Copy region (LSC; 66,903 bp), Small Single Copy region (SSC; 17,490), and an Inverted Repeat (IR; 17,332) (Table 1; Fig. 1). The H. warnockii plastome is thus 29,902 bp smaller than the leafy orchid P. equestris, or approximately 79.9% the total size of the latter (148,959 bp, representing a typical orchid plastome size). The largest physical reduction in the H. warnockii plastome was in the LSC Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii region, which was 27.6% smaller than that of P. equestris due to several large deletions. There is a contraction of the inverted repeat (IR) in H. warnockii, representing a 33% difference in total IR length relative to P. equestris. This contraction resulted in the following genes, typically GAU UGC found in the IR, becoming part of the SSC: 16S rRNA, trnI , trnA , 23S rRNA, 4.5S rRNA, ACG GUU 5S rRNA, trnR , trnN , and the 5’ portion of ycf1. Total GC content is 36.9% after removing one copy of the IR, and similar to that of Phalaenopsis at 36.7%. We identified 45 dispersed repeats across the genome passing our filters in REPuter: two were forward-compliment, 16 forward-forward, 22 palindromic, and five forward-reverse (Table 2). We identified 419 tandem repeats with minimum motif lengths of 10 bp (Table 2; Table S1). The most abundant of these were hexanucleotide repeats (141) followed by pentanucleotide repeats (99). We identified three dinucleotide repeats, 17 trinucleotide repeats, and 50 tetranucleotide repeats. Thus, there are several options for the development of potentially variable satellite markers in H. warnocki, which will be useful in determining patterns of plastid genomic diversity across populations of this endangered orchid. Alignment with MAUVE detected a major genomic inversion of a ~29 kb region of the LSC relative to P. equestris with GCU GGA breakpoints spanning trnS and trnS ; the entire collinear block detected by MAUVE contains 29 genes (Fig. 1). The plastome of H. warnockii encodes 72 putatively functional genes (protein-coding, tRNA, and rRNA), compared to 103 in P. equestris, a 31.1% difference in functional gene content, composed of pseudogenes (i.e. functional losses, 25 in H. warnockii relative to P. equestris) and physical gene losses (11 in H. warnockii relative to P. equestris). The total plastome size reduction in H. warnockii is largely due to the deletion of regions containing photosynthesis-related genes (Fig. 1), thus also reducing the gene count. Plastome size in H. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii warnockii is comparable to that of the mycoheterotrophic orchid Corallorhiza striata var. vreelandii at 137,505 bp (Barrett and Davis, 2012), and to the holoparasite Myzorhiza californica at 120,840 bp (Wicke et al., 2013; see Fig. 2). Overall there is a strong positive correlation between the number of putatively functional genes and plastome length among heterotrophic angiosperms (Fig. 2; Pearson correlation r = 0.953, p < 0.0001); thus, physical gene loss is at least in part driving a reduction in plastome size. Genes that are either functionally or physically lost conform to the models of Barrett and Davis (2012), Wicke et al. (2016) and Graham et al. (2017), and include: photosynthesis-related genes [Photosystem I and I subunits (psa, psb), Cytochrome subunits (pet), RuBisCO Large Subunit (rbcL), Photosystem Assembly Factors (ycf3, ycf4, also called paf1 and paf2 respectively; Wicke et al., 2011); subunits of the plastid-encoded RNA Polymerase (rpo); and subunits of the ATP synthase complex (atp). There are also substantial functional and physical losses among subunits of the NAD(P)H Dehydrogenase complex (ndh; all physically lost except ndhK, ψndhB, and ψndhC), but this is common in other orchids including Phalaenopsis, perhaps due to the tendency of orchids to occupy low-light environments (e.g. Lin et al., 2017). Losses in subunits of these functional gene categories conform to ‘stage 4’ of the model of plastome degradation by Barrett and Davis (2012), and are also in line with a recent mechanistic model of plastome evolution (Wicke et al. 2016). Functional loss of five out of six ATP Synthase subunit genes is significant, in that many parasitic lineages early in the process of plastome degradation tend to have preserved reading frames for atp genes despite having experienced major losses in photosynthesis-related and rpo genes (Barrett et al., 2014; Wicke et al., 2016; Braukmann et al., 2017; Graham et al., 2017). Thus, H. warnockii may have entered a Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii new phase in plastome evolution following a period of evolutionary stasis, based on the ‘punctuated burst’ model of plastome evolution put forth by Naumann et al. (2016). The IR is hypothesized to function in plastid genome structural stability, but studies from highly rearranged genomes are equivocal (Palmer, 1995; Lam et al. 2015; Lim et al., 2015). Here, a 29 kb LSC inversion is found in conjunction with a drastic reduction of the IR (Fig. 1). Repeats have been shown in parasitic Orobanchaceae to be associated with plastome structural rearrangements and shifts in IR boundaries (Wicke et al. 2013); thus additional sampling of Hexalectris spp. and related genera will allow for explicit tests among repeat content, structural rearrangements, and substitution rates. The ancestor of Hexalectris may have been evolving under relaxed selective pressure for up to 32 million years, based on a stem-node age estimate of Hexalectris, which also includes members of the closely related genera Basiphyllaea and Bletia (Sosa et al., 2016). Hexalectris warnockii is consistently placed as sister to the remaining members of genus Hexalectris in previous studies (Kennedy and Watson, 2010; Sosa et al., 2016); thus it is unknown whether this species has undergone an independent transition to full mycoheterotrophy, or if this condition is shared by all species in the genus. Regardless, plastome degradation has been occurring in H. warnockii for an estimated 24 million years, when the first divergence occurred within Hexalectris (Sosa et al., 2016). Sequencing of additional members of Hexalectris, and the closely related members of tribe Bletiinae (Basiphyllaea, Bletia) will allow fine-scale reconstruction of plastid genome degradation, and testing of the hypothesis of a single origin of full mycoheterotrophy/loss of photosynthesis in Hexalectris. Furthermore, sampling of multiple individuals per species may uncover substantial variation in plastomes across the geographic Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii range of each species, as has been recently demonstrated in the fully mycoheterotrophic orchid Corallorhiza striata (Barrett et al., 2018). ACKNOWLEDGEMENTS We thank Big Bend National Park (US Department of Interior) for permission and assistance in collecting material; this research was supported by the West Virginia University Program to Stimulate Competitive Research Grant to CB. We thank two anonymous reviewers for suggestions that improved the manuscript. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii LITERATURE CITED Barrett CF, Davis JI. 2012. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. American Journal of Botany 99: 1513-1523. Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, et al. 2014. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution 31: 3095-3112. Barrett CF, Wicke S, Sass C. 2018. Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex. New Phytologist, in press. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. Braukmann TWA, Broe MB, Stefanović S, Freudenstein JV. 2017. On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae. New Phytologist 216: 254-266. Catling, P.M. 2004. A synopsis of the genus Hexalectris in the United States and a new variety of Hexalectris revoluta. The Native Orchid Conference Journal 1: 5-25. Catling, P. M. and V. S. Engel. 1993. Systematics and distribution of Hexalectris spicata var. arizonica (Orchidaceae). Lindleyana 8: 119–125. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147. https://doi.org/10.1371/journal.pone.0011147. Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii genomes from whole genome data. Nucleic Acids Research 45: e18. https://doi:10.1093/nar/gkw955. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15. Freudenstein JV. 1999. A new species of Corallorhiza (Orchidaceae) from West Virginia, USA. Novon 9: 511-513. Freudenstein JV, Barrett CF. 2010. Mycoheterotrophy and diversity in Orchidaceae. In: Seberg O, Petersen G, Barfod A, Davis JI, editors. Diversity, phylogeny and evolution in the monocotyledons. The Proceedings of the Fourth International Conference on Monocot Systematics. Aarhus (Denmark): Aarhus University Press. p. 25-37. Glenn TC, Nilsen R, Kieran TJ, Finger JW, Pierson TW, et al. 2016. Adapterama I: Universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru &amp; iNext). BioRxiv 049114. https://doi.org/10.1101/049114. Goedeke, T., Sharma, J., Treher, A., Frances, A. & Poff, K. 2015. Hexalectris warnockii. The IUCN Red List of Threatened Species 2015: http://dx.doi.org/10.2305/IUCN.UK.2015-4.RLTS.T64176203A64176207.en. Graham SW, Lam VK, Merckx VS. 2017. Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes. New Phytologist 214: 48-55. Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4: 1-9. Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772-780. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649. Kennedy AH, Taylor DL, Watson LE. 2011. Mycorrhizal specificity in the fully mycoheterotrophic Hexalectris Raf. (Orchidaceae: Epidendroideae). Molecular Ecology 20: 1303-1316. Kennedy AH, Watson LE. 2010. Species delimitations and phylogenetic relationships within the fully myco-heterotrophic Hexalectris (Orchidaceae). Systematic Botany 35: 64- Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29: 4633-4642. Lam VK, Soto Gomez M, Graham SW. 2015. The highly reduced plastome of mycoheterotrophic Sciaphila (Triuridaceae) is colinear with its green relatives and is under strong purifying selection. Genome Biology and Evolution 7: 2220-2236. Lim GS, Barrett CF, Pang CC, Davis JI. 2016. Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri. American Journal of Botany 103: 1129-1137. Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, et al. 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant Journal 90: 994- Lohse M, Drechsel O, Kahlau S, Bock R. 2013. OrganellarGenomeDRAW-a suite of tools Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41: W575-W581. Mayer C. 2010. Phobos 3.3.11. http://www.rub.de/ecoevo/cm/cm_phobos.htm. Merckx V, Freudenstein JV. 2010. Evolution of mycoheterotrophy in plants: a phylogenetic perspective. New Phytologist 185: 605-609. Merckx VSFT, Smets EF, Specht CD. 2013. Biogeography and conservation of mycoheterotrophic plants. Merckx V, editor. Mycoheterotrophy: The Biology of Plants Living on Fungi. New York: Springer. p. 103-156. Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, et al. 2016. Detecting and characterizing the highly divergent plastid genome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae). Genome Biology and Evolution 8: 345-363. Palmer JD. 1985. Comparative organization of chloroplast genomes. Annual Review of Genetics 19: 325-354. R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/. Sosa V, Cameron KM, Angulo DF, Hernandez-Hernandez T. 2016. Life form evolution in epidendroid orchids: Ecological consequences of the shift from epiphytism to terrestrial habit in Hexalectris. Taxon 65: 235-248. Taylor DL, Bruns TD, Szaro TM, Hodges SA. 2003. Divergence in mycorrhizal specialization within Hexalectris spicata (Orchidaceae), a nonphotosynthetic desert orchid. American Journal of Botany 90: 1168-1179. Taylor DL, Barrett C, Beatty G, Kennedy A, Klooster M, et al. 2013. Progress and prospects for the ecological genetics of mycoheterotrophs. pp 245-266 In Mycoheterotrophy: Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii The Biology of Plants Living on Fungi. Merckx V, editor. New York: Springer. p. 245-266. Wicke S, Schneeweiss GM, dePamphilis CW, Muller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology 76: 273-297. Wicke S, Muller KF, de Pamphilis CW, Quandt D, Wickett NJ, et al. 2013. Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. Plant Cell 25: 3711-3725. Wicke S, Muller KF, dePamphilis CW, Quandt D, Bellot S, et al. 2016. Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences of the United States of America 113: 9045-9050. Wolfe KH, Morden CW, Palmer JD. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences of the United States of America 89: 10648-10652. Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Table 1. Features of the fully mycoheterotrophic Hexalectris warnockii plastid genome relative to that of the leafy, autotrophic Phalaenopsis equestris (GenBank accession JF719062). Hexalectris Phalaenopsis % of warnockii equestris Phalaenopsis Total Length (bp) 119,057 148,959 79.9 Large single copy (LSC) 66,903 85,967 77.8 Inverted repeat (IR) 17,332 25,846 67.1 Small single copy (SSC) 17,490 11,300 154.8 protein coding genes (CDS) 38 69 55.1 Pseudogenes (ψ) 25 3 833.3 Transfer RNA genes (tRNA) 30 30 93.3 Ribosomal RNA genes (rRNA) 4 4 100.0 Putatively functional 72 103 69.9 Total genes & pseudogenes 97 106 91.5 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii Table 2. Numbers of dispersed and tandem repeats detected with REPuter and Phobos, respectively. Tandem repeat sequences are listed in Table S1. Dispersed repeats Repeat type number forward-compliment 2 forward-forward 16 palindromic 22 forward-reverse 5 Tandem repeats Motif length (bp) number 2 3 3 17 4 50 5 99 6 141 7 50 8 19 9 15 >9 25 Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Genome Report: plastid genome degradation in the endangered Hexalectris warnockii FIGURE LEGENDS Fig. 1. Map of the plastid genome of Hexalectris warnockii. ‘LSC’ = large single copy region; ‘SSC’ = small single copy region; gray = inverted repeat; dashed line in LSC = a 29 kb inversion. Red text indicates the presence of a pseudogene (ψ). ‘*’ and “**’ denote genes with one or two introns, respectively. Fig. 2. A comparison of plastid genome size and the number of putatively functional genes for sequenced holoparasites (gray), full mycoheterotrophs (black), and selected autotrophs (including partial mycoheterotrophs and hemiparasites; green), with trophic status based on whether or not photosynthetic genes are putatively functional in each. Inset: Hexalectris warnockii in flower (photo: A. Kennedy; Big Bend National Park, Brewster Co., TX, USA). Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 photosystem I RubisCO large subunit ycf genes Hexalectris warnockii photosystem II RNA polymerase ORFs cytochrome b/f complex ribosomal proteins (SSU) transfer RNAs chloroplast genome 10kb ATP synthase ribosomal proteins (LSU) ribosomal RNAs NADH dehydrogenase accD, clpP, matK (ψ) = pseudogene 119,057 bp *, ** = intron(s) LSC Inverted Repeat A ycf2 ycf1 ycf2 Inverted SSC Repeat B Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 psbA(ψ) mat K trnK-UUU rps16* trnQ-UUG psbK(ψ) trnS-GCU ycf3 (ψ) psaA(ψ) psaB(ψ) rps1 4 trnG-UCC trnfM-CAU trnS-CGA psbZ psbC(ψ) psbD(ψ) trnT-GGU trnE-UUC trnY-GUA trnD-GUC petN(ψ) psbM trnC-GCA rpoC1(ψ) rpoC2(ψ) rps2 atpI(ψ) atpH atpF(ψ) atpA(ψ) trnR-UCU trnG-UCC* trnS-GCU rps4 trnL-UAA* trnT-UGU ndhK ndhC(ψ) trnF-GAA trnV-UAC* trnM-CAU atpE(ψ) rbcL(ψ) atpB(ψ) accD psaI ycf4(ψ) cemA(ψ) psbJ petA(ψ) psbL pet L psbF psbE pet G trnW-CCA rpl3 3 trnP-UGG rps18 rpl20 rps12(5’) clpP** psbB(ψ) rpoA(ψ) petD(ψ) rps11 rpl3 6 rps8 rpl14 rpl16 rps3 rpl22 trnH-GUG rps1 9 rpl2* rpl23 trnI-CAU trnL-CAA ndhB(ψ) rps7 rps12_3end rpl3 2 trnL-UAG ccsA(ψ) trnV-GAC 16S rRNA trnI-GAU* trnA-UGC* 23S rRNA 4.5S rRNA 5S rRNA trnR-ACG trnN-GUU rpl32 (partial) rps15 rps12 (3’)* rps7 ndhB(ψ) trnL-GAG trnI-CAU rpl23 rpl2* trnH-GUG rps19 rpl22 rps3 Leafy, partially mycoheterotrophic, and hemiparasitic taxa Cuscuta exaltata Cuscuta reflexa Cuscuta obtusiflora Hexalectris Corallorhiza mertensiana Corallorhiza mac. maculata warnockii Cuscuta Corallorhiza Corallorhiza mac. occidentalis gronovii striata Lathraea squamaria Myzorrhiza californica Aphyllorchis montana Petrosavia stellaris Neottia camtschatea Neottia acuminata Phelipanche Neottia listeroides purpurea Orobanche crenata 60 Orobanche Cistanche phelypaea gracilis Neottia nidus-avis Phelipanche Conopholis ramosa Boulardia latisquama americana Epifagus Hypopitys virginiana monotropa Sciaphila Rhizanthella gardneri densiflora Epipogium Holoparasite roseum Epipogium aphyllum Full mycoheterotroph Cytinus hypocistis Hydnora visseri Leafy, partial mycoheterotroph, or hemiparasite Thismia tentaculata Pilostyles hamiltonii Pilostyles aethiopica 0 30000 60000 90000 120000 150000 160000 Length of plastome (bp) Downloaded from https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evy107/5020730 by Ed 'DeepDyve' Gillespie user on 07 June 2018 Number of putatively functional genes

Journal

Genome Biology and Evolution – Oxford University Press

Published: May 29, 2018

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