Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

doi:10.1016/j.pld.2021.01.002

Abstract

Abstract: Corallorhiza sinensis, a new species of mycoheterotrophic orchid from western Sichuan, China, is described and illustrated based on molecular and morphological evidence. It is morphologically similar to Corallorhiza trifida, but can be distinguished by bigger flowers, both sepals and petals with 3 veins, and longer lateral lobes of lip. To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae, this study employed sequences of the nuclear ribosomal DNA (nrDNA) and whole plastome assembled from the genome skimming approach. The plastome is 148,124 bp in length, including a pair of inverted repeats (IRs) of 26,165 bp, a large single-copy region (LSC) of 82,207 bp, and a small single-copy region (SSC) of 13,587 bp. Further, phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences (CDSs) from 26 complete plastomes of subtribe Calypsoinae. The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group, and strongly support C. sinensis as sister to the rest species of Corallorhiza. The plastid tree showed that 10 Corallorhiza species grouped into two clades and C. sinensis is most closely related to the North American C. striata and C. bentleyi instead of Oreorchis foliosa and O. angustata in the same clade. The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic. Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C. sinensis, it is still the most closely related to Corallorhiza. Comparative analysis showed that C. sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis. The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.

Key words: Corallorhiza sinensis, Oreorchis, Sichuan province, Plastome, Phylogeny

Jia-Xin Yang, Shuai Peng, Jun-Jie Wang, Shi-Xiong Ding, Yan Wang, Jing Tian, Han Yang, Guang-Wan Hu, Qing-Feng Wang. Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China[J]. Plant Diversity, 2021, 43(05): 409-419.

References

Bankevich, A., Nurk, S., Antipov, D., et al., 2012. SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. https://doi.org/10.1089/cmb.2012.0021.
Barrett, C.F., Davis, J.I., 2012. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. Am. J. Bot. 99, 1513-1523. https://doi.org/10.3732/ajb.1200256.
Barrett, C.F., Freudenstein, J.V., Jeff, L., et al., 2014. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Mol. Biol. Evol. 31, 3095-3112. https://doi.org/10.1093/molbev/msu252.
Camacho, C., Coulouris, G., Avagyan, V., et al., 2009. BLAST+:architecture and applications. BMC Bioinf. 10, 421. https://doi.org/10.1186/1471-2105-10-421.
Chase, M.W., Cameron, K.M., Freudenstein, J.V., et al., 2015. An updated classification of Orchidaceae. Bot. J. Linn. Soc. 177, 151-174. https://doi.org/10.1111/boj.12234.
Chen, X.Q., Gale, S.W., Cribb, P.J., 2009. Corallorhiza. In:Wu, Z.Y., Raven, P.H., Hong, D.Y. (Eds.), Flora of China, vol. 25. Beijing:Science Press; St. Louis:Missouri Botanical Garden Press, pp. 252-253.
Christenhusz, M.J.M., Byng, J.W., 2016. The number of known plants species in the world and its annual increase. Phytotaxa 261, 201-217. https://doi.org/10.11646/phytotaxa.261.3.1.
Darling, A.C.E., Mau, B., Blattner, F.R., et al., 2004. Mauve:multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403. https://doi.org/10.1101/gr.2289704.
Freudenstein, J.V., 1997. A monograph of Corallorhiza (Orchidaceae). Harv. Pap. Bot. 1, 5-51. https://doi.org/10.2307/41761525.
Freudenstein, J.V., 1999. A new species of Corallorhiza (Orchidaceae) from West Virginia. U.S.A. Novon 9, 511-513. https://doi.org/10.2307/3392151.
Freudenstein, J.V., Senyo, D.M., 2008. Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae:Epidendroideae). Am. J. Bot. 95, 498-505. https://doi.org/10.3732/ajb.95.4.498.
Freudenstein, J.V., Yukawa, T., Luo, Y.B., 2017. A reanalysis of relationships among Calypsoinae (Orchidaceae:Epidendroideae):floral and vegetative evolution and the placement of Yoania. Syst. Bot. 42, 17-25. https://doi.org/10.1600/036364417x694944.
Jin, J.J., Yu, W.B., Yang, J.B., et al., 2020. GetOrganelle:a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21, 241. https://doi.org/10.1186/s13059-020-02154-5.
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., et al., 2017. ModelFinder:fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587-589. https://doi.org/10.1038/nmeth.4285.
Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Mol. Biol. Evol. 30, 772-780. https://doi.org/10.1093/molbev/mst010.
Kearse, M., Moir, R., Wilson, A., et al., 2012. Geneious Basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649. https://doi.org/10.1093/bioinformatics/bts199.
Khayi, S., Gaboun, F., Pirro, S., et al., 2020. Complete chloroplast genome of Argania spinosa:structural organization and phylogenetic relationships in sapotaceae. Plants 9. https://doi.org/10.3390/plants9101354.
Kim, Y.K., Jo, S., Cheon, S.H., et al., 2020. Plastome evolution and phylogeny of Orchidaceae, with 24 new sequences. Fron. Plant Sci. 11, 22. https://doi.org/10.3389/fpls.2020.00022.
Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870-1874. https://doi.org/10.1093/molbev/msw054.
Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359. https://doi.org/10.1038/nmeth.1923.
Lee, S.Y., Meng, K., Wang, H., et al., 2020. Severe plastid genome size reduction in a mycoheterotrophic orchid, Danxiaorchis singchiana, reveals heavy gene loss and gene relocations. Plants 9, 521. https://doi.org/10.3390/plants9040521.
Li, Z.H., Jiang, Y., Ma, X., et al., 2020. Plastid genome evolution in the subtribe Calypsoinae (Epidendroideae, Orchidaceae). Genome Biol. Evol. 12, 867-870. https://doi.org/10.1093/gbe/evaa091.
Lohse, M., Drechsel, O., Bock, R., 2007. OrganellarGenomeDRAW (OGDRAW):a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52, 267-274. https://doi.org/10.1007/s00294-007-0161-y.
Macdougal, D.T.,Dufrenoy,J.,1944. Mycorrhizalsymbiosis in Aplectrum,Corallorhizaand Pinus. Plant Physiol. (Wash. D C) 19, 440-465. https://doi.org/10.2307/4257795.
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., et al., 2015. IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32 (1), 268-274. https://doi.org/10.1093/molbev/msu300.
Pearce, N., Cribb, P., 1997. A revision of the genus Oreorchis (Orchidaceae). Edinb. J. Bot. 54, 289-328. https://doi.org/10.1017/S0960428600004145.
Qu, X.J., Moore, M.J., Li, D.Z., et al., 2019. PGA:a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods 15, 50. https://doi.org/10.1186/s13007-019-0435-7.
Ronquist, F., Teslenko, M., van der Mark, P., et al., 2012. MrBayes 3.2:efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542. https://doi.org/10.1093/sysbio/sys029.
Suetsugu, K., Haraguchi, T.F., Tanabe, A.S., et al., 2020. Specialized mycorrhizal association between a partially mycoheterotrophic orchid Oreorchis indica and a Tomentella taxon. Mycorrhiza. https://doi.org/10.1007/s00572-020-00999-z.
Talavera, G., Castresana, J., 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577. https://doi.org/10.1080/10635150701472164.
Wick, R.R., Schultz, M.B., Zobel, J., et al., 2015. Bandage:interactive visualization of de novo genome assemblies. Bioinformatics 31, 3350-3352. https://doi.org/10.1093/bioinformatics/btv383.
Wu, L.W., Nie, L.P., Xu, Z.C., et al., 2020. Comparative and phylogenetic analysis of the complete chloroplast genomes of three Paeonia section Moutan species(Paeoniaceae). Front. Genet. 11 https://doi.org/10.3389/fgene.2020.00980.
Yukawa, T., Chung, S.W., Luo, Y.B., et al., 2003. Reappraisal of Kitigorchis (Orchidaceae). Bot. Bull. Acad. Sin. (Taipei) 44, 345-351.
Zhai, J.W., Zhang, G.Q., Chen, L.J., et al., 2013. A new orchid genus, Danxiaorchis, and phylogenetic analysis of the tribe Calypsoeae. PLoS One 8, e60371. https://doi.org/10.1371/journal.pone.0060371.
Zhang, D., Gao, F.L., Jakovlic, I., et al., 2020. PhyloSuite:an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour. 20, 348-355. https://doi.org/10.1111/1755-0998.13096.
Zhu, B., Feng, Q., Yu, J., et al., 2020. Chloroplast genome features of an important medicinal and edible plant:Houttuynia cordata (Saururaceae). PLoS One 15, e0239823. https://doi.org/10.1371/journal.pone.0239823.
Zimmer, K., Meyer, C., Gebauer, G., 2008. The ectomycorrhizal specialist orchid Corallorhiza trifida is a partial myco-heterotroph. New Phytol. 178, 395-400.https://doi.org/10.1111/j.1469-8137.2007.02362.x.

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