Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

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...

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Autores principales:	Niu Zhitao, Zhu Shuying, Pan Jiajia, Li Ludan, Sun Jing, Ding Xiaoyu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f025e611891749e49441ba0a4e0ac4e2
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spelling	oai:doaj.org-article:f025e611891749e49441ba0a4e0ac4e22021-12-02T15:06:20ZComparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots10.1038/s41598-017-02252-82045-2322https://doaj.org/article/f025e611891749e49441ba0a4e0ac4e22017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02252-8https://doaj.org/toc/2045-2322Abstract 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 hotspots—trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ—should be used in the phylogenetic and identification studies of Dendrobium.Niu ZhitaoZhu ShuyingPan JiajiaLi LudanSun JingDing XiaoyuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Niu Zhitao Zhu Shuying Pan Jiajia Li Ludan Sun Jing Ding Xiaoyu Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
description	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 hotspots—trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ—should be used in the phylogenetic and identification studies of Dendrobium.
format	article
author	Niu Zhitao Zhu Shuying Pan Jiajia Li Ludan Sun Jing Ding Xiaoyu
author_facet	Niu Zhitao Zhu Shuying Pan Jiajia Li Ludan Sun Jing Ding Xiaoyu
author_sort	Niu Zhitao
title	Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
title_short	Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
title_full	Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
title_fullStr	Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
title_full_unstemmed	Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots
title_sort	comparative analysis of dendrobium plastomes and utility of plastomic mutational hotspots
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f025e611891749e49441ba0a4e0ac4e2
work_keys_str_mv	AT niuzhitao comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots AT zhushuying comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots AT panjiajia comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots AT liludan comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots AT sunjing comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots AT dingxiaoyu comparativeanalysisofdendrobiumplastomesandutilityofplastomicmutationalhotspots
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Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

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