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

BMC Evolutionary Biology

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[1] 0000 0001 2182 8825, grid.260463.5, Nanchang University, Xuefu Road 999, Honggutang District, Nanchang, Jiangxi, China;0000000119573309, grid.9227.e, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China;0000000119573309, grid.9227.e, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China;0000 0004 1797 8419, grid.410726.6, University of Chinese Academy of Sciences, Beijing, China;0000000119573309, grid.9227.e, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China;Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Nay Pyi Taw, Myanmar;Fujian Agriculture and Forest University, Shanxiadian Road 15, Changshan District, 350002, Fuzhou, Fujian, China;

关键词: Holcoglossum;    Plastid genome;    NDH complex;    Divergence hotspot;    Intraspecific variation;    Tandem repeat;    Hairpin inversion;   

DOI  :  10.1186/s12862-019-1384-5

来源: publisher

【 摘 要 】

BackgroundThe 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.ResultsIn 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.ConclusionsUsing 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.

【 授权许可】

CC BY