Abstract
The first complete plastid genome of Cheirostylis, Ch. chinensis, was assembled and analyzed in this study. The total genome was 147,218 bp in length, consisting of a large single-copy region (LSC) of 81,081 bp, a small single-copy region (SSC) of 14,769 bp, and two inverted repeat regions (IRA and IRB) of 25,684 bp. The genome contained 131 genes, including 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes. Phylogenomic analysis indicated that Ch. chinensis nested within Goodyerinae.
Keywords: Chloroplast genome, Cranichideae, Orchidoideae, phylogeny
Introduction
The genus Cheirostylis, belonging to the subtribe Goodyerinae (Orchidaceae, Orchidoideae, Cranichideae), is characterized by the fleshy and moniliform rhizome with internodal rhizoids, flowers with obconical ovaries, connate sepals, a lip containing parallel seriate appendages, and a column with two separate stigma lobes that bear sterile extensions (Pridgeon et al. 2003; Chen et al. 2019). The genus consists of approximately 55 species well represented in tropical Africa, Asia and the Pacific Islands (Govaerts et al. 2012).
In this study, a complete plastid genome of Cheirostylis, Ch. chinensis, was assembled and annotated. The complete genomic DNA was extracted from fresh leaves using a modified Cetyltrimethylammonium Ammonium Bromide (CTAB) method (Doyle and Doyle 1987) and sequenced by the BGISEQ-500 platform. The samples were collected from Jinan district, Fujian, China (26°38′N, 119°27′E) and the voucher specimen deposited at Herbarium of Fujian Agriculture and Forestry University (specimen code FJFC 0411). The clean reads were used to assemble the complete chloroplast genome by the GetOrganelle pipe-line (Jin et al. 2018), with the chloroplast genome of Goodyera procera (GenBank accession KT886429) as the reference sequences. The assembled chloroplast genome was annotated using the Geneious R11.15 (Kearse et al. 2012).
The total chloroplast genome of Ch. chinensis (GenBank accession MN641483) was 147,218 bp in length, consisting of a large single-copy region (LSC) of 81,081 bp, a small single-copy region (SSC) of 14,769 bp, and two inverted repeat regions (IRA and IRB) of 25,684 bp. The GC content of the chloroplast genome was 36.79%, while the corresponding values of the LSC, SSC, and IR regions are 34.32%, 29.00%, and 42.93%, respectively. The complete chloroplast genome contains 131 genes, including 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes.
To confirm the phylogenetic position of Ch. chinensis, a phylogenetic analysis was performed based on 12 species of Orchidoideae and two outgroup species of Cypripedioideae. All sequences were aligned with the HomBlock pipeline (Bi et al. 2018), and the phylogenetic tree constructed by RAxML (Stamatakis 2014) with 1000 ultrafast bootstrap (UFBoot) replicates (Minh et al. 2013; Chernomor et al. 2016). The results showed that Ch. chinensis nested within Goodyerinae (Figure 1).
Figure 1.
The maximum-likelihood (ML) tree based on the 12 representative plastid genome sequences of Orchidoideae and two outgroup species of Cypripedioideae. The bootstrap value near each node.
Funding Statement
Nature Science Foundation of Fujian Province, China [2018J01698].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Bi G, Mao Y, Xing Q, Cao M. 2018. HomBlocks: a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics. 110(1):18–22. [DOI] [PubMed] [Google Scholar]
- Chen SP, Tian HZ, Guan QX, Zhai JW, Zhang GQ, Chen LJ, Liu ZJ, Lan SR, Li MH. 2019. Molecular systematics of Goodyerinae (Cranichideae, Orchidoideae, Orchidaceae) based on multiple nuclear and plastid regions. Mol Phylogenet Evol. DOI: 10.1016/j.ympev.2019.106542 [DOI] [PubMed] [Google Scholar]
- Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 65(6):997–1008. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
- Govaerts R, Pfahl J, Campacci MA, Holland Baptista D, Tigges H, Shaw J, Cribb P, George A, Kreuz K, Wood J. 2012. World Checklist of Orchidaceae. The Board of Trustees of the Royal Botanic Gardens, Kew; [accessed 2018 April 10]. http://www.kew.org/wcsp/
- Jin JJ, Yu WB, Yang JB, Song Y, Yi TS, Li DZ. 2018. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. BioRxiv. 4:256479. [Google Scholar]
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pridgeon AM, Cribb PJ, Chase MW, Rasmussen FN. 2003. Genera orchidacearum Vol. 3, Orchidoideae (part two), Vanilloideae. Oxford (UK): Oxford University Press; p. 77. [Google Scholar]
- Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]