Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Scientific Reports
Niu ZhitaoDing Xiaoyu

Abstract

Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotsp...Continue Reading

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Citations

Nov 4, 2017·International Journal of Molecular Sciences·Zhitao NiuXiaoyu Ding
Feb 28, 2019·BMC Evolutionary Biology·Zhang-Hai LiXiao-Hua Jin
Aug 2, 2018·Planta·Shi-Gang ZhengZe Chun
Nov 28, 2020·Scientific Reports·Chung-Shien WuShu-Miaw Chaw
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Liu WeiDing Xiaoyu
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Shi-Cheng ShaoYan Luo

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Methods Mentioned

BETA
PCR

Software Mentioned

DOGMA
DnaSP
RAxML
SPSS Statistics
SE
GMATo
Mega
MUSCLE
tRNAscan
SequenceMatrix

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