Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

Abstract

Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation . This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. Results In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh -gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. Conclusions Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1384-5) contains supplementary material, which is available to authorized users.

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

“…For examples, extensive gene losses have been reported in several independent mycoheterotrophic orchid lineages-i.e., Aphyllorchis (Feng et al, 2016), Cyrtosia (Kim et al, 2019), Epipogium (Schelkunov et al, 2015), Gastrodia (Yuan et al, 2018), Hexalectris (Barrett and Kennedy, 2018) and Rhizanthella (Delannoy et al, 2011). In addition, ndh deletion and pseudogenization are assumed to be phenomena that occur independently in many orchid lineages such as Apostasia (Lin et al, 2017;Niu et al, 2017a), Calypso , Cattleya (da Rocha Perini et al, 2016), Cephalanthera (Feng et al, 2016), Cremastra (Dong et al, 2018), Cymbidium (Yang et al, 2013;Kim et al, 2018;Wang et al, 2018), Dendrobium (Niu et al, 2017b), Epipactis (Dong et al, 2018), Eulophia (Huo et al, 2017), Holcoglossum (Li et al, 2019), Limodorum (Lallemand et al, 2019), Liparis (Krawczyk et al, 2018), Neuwiedia (Niu et al, 2017a), Oncidium (Wu et al, 2010;Kim et al, 2015a), Paphiopedilum (Niu et al, 2017b;Hou et al, 2018), Phalaenopsis (Chang et al, 2006), Phragmipedium (Kim et al, 2015a), Platanthera (Dong et al, 2018), Vanilla (Lin et al, 2015), and Vanda (Li et al, 2019). On the other hand, full ndh genes have been reported in members of Anoectochilus (Yu et al, 2016), Calanthe (Dong et al, 2018), Cypripedium (Kim et al, 2015b;Lin et al, 2015), Habenaria…”

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…Based on the SSR polymorphism results, we found 82 SSRs in the Q. bawanglingensis cp genome. Most of the SSRs are distributed in the LSC region (62, 75.61%), followed by the SSC region (16,19.51%) and IRs (4, 4.88%), whereas 64 are located in intergenic spaces and 18 in genes, such as trnK-UUU, trnG-GC, atpF, rpoC2, rpoC1, rpoB, atpB, accD, clpP, petB, petD, ndhF, ndhD, ndhA and ycf1 (Table A6). Furthermore, rpoC1 and rpoC2 contain more SSR loci than the other genes.…”

“…Due to its uniparental inheritance, highly conserved structure, general lack of recombination and small effective population size, the analysis of cp DNA has been deemed a useful method for evolution research and the exploration of plant systematics [6][7][8][9]. In fact, the availability of sufficient data on cp genomes is crucial for phylogenetic relationship reconstruction, i.e., the assessment of relationships within angiosperms [10][11][12], the identification of members of Pinaceae [13] and Pinus [14], and adequate comparisons, i.e., cp genomes from sister species [15] and possibly multiple individuals [16]. At present, approximately 3000 plastid genomes of Eukaryota are shareable in the National Center for Biotechnology Information database (NCBI; Available online: https: //www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=plastid&taxid=2759&sort=Genome) due to improvements in sequencing technologies.…”

Phylogenomics and biogeography of Wisteria (Fabaceae), with implication on plastome evolution of inverted repeat-lacking clade

“…The plastomes of most vascular plants usually have a conservative quartile structure with a large single-copy (LSC) region and a small single-copy (SSC) region separated by two inverted repeat (IR) 3 regions [1][2][3][4][5]. They are about 150 kb in size and contain around 114 unique genes, including four rRNA genes, 30 tRNA genes, and 80 protein genes [6].…”

“…Previous studies support the reciprocal monophyly of eastern Asian and eastern North American species, but the interspecific relationships of Asian species have not been resolved [37], largely due to the small amount of data. Plastomes have been widely used in phylogenetic studies of closely related species [1,4,9,41]. Within Wisteria, plastomes of W. sinensis and W. floribunda have been reported before [42].…”