The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

Frontiers in Plant Science
Zhi-Tao NiuXiao-Yu Ding

Abstract

Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5'trnK-rps16, trnS-...Continue Reading

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Citations

Nov 4, 2017·International Journal of Molecular Sciences·Zhitao NiuXiaoyu Ding
Jan 16, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yongfu LiXianrong Wang
Jun 10, 2020·Molecular Biology Reports·Fenxiang LiuYu Zhang
Feb 28, 2019·BMC Evolutionary Biology·Zhang-Hai LiXiao-Hua Jin
Nov 11, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xin ZhangManrang Zhang
Aug 2, 2018·Planta·Shi-Gang ZhengZe Chun
Apr 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Cuihua GuZhiqiang Wu
Mar 11, 2020·Frontiers in Plant Science·Young-Kee KimKi-Joong Kim
Jul 29, 2020·Frontiers in Plant Science·Michelle Zavala-PáezEric de Camargo Smidt
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Aug 23, 2019·International Journal of Molecular Sciences·Yingxian CuiHui Yao
Oct 22, 2020·PeerJ·Yanqiong ChenJunwen Zhai
Aug 20, 2021·Mitochondrial DNA. Part B, Resources·Mengting WangXiaoyu Ding
Aug 31, 2021·3 Biotech·Shanmugavel SenthilkumarModhumita Ghosh Dasgupta
Oct 12, 2021·Frontiers in Plant Science·Ling ZhangZhao-Yang Chang

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Methods Mentioned

BETA
PCR

Software Mentioned

DnaSP
DOGMA
Mayas
RAxML
PartitionFinder
blastn
SE
GMATo
MUSCLE
tRNAscan

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