Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poo...

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Autores principales:	Hanqing Tang, Lu Tang, Shicheng Shao, Yulan Peng, Lu Li, Yan Luo
Formato:	article
Lenguaje:	EN
Publicado:	KeAi Communications Co., Ltd. 2021
Materias:	Chloroplast genome Sequence divergence DNA markers SSR Bulbophyllum Orchidaceae Biology (General) QH301-705.5 Botany QK1-989
Acceso en línea:	https://doaj.org/article/2cb0378b6426430db05913e6072fb157
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spelling	oai:doaj.org-article:2cb0378b6426430db05913e6072fb1572021-11-12T04:43:51ZChloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution2468-265910.1016/j.pld.2021.01.003https://doaj.org/article/2cb0378b6426430db05913e6072fb1572021-10-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2468265921000032https://doaj.org/toc/2468-2659Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.Hanqing TangLu TangShicheng ShaoYulan PengLu LiYan LuoKeAi Communications Co., Ltd.articleChloroplast genomeSequence divergenceDNA markersSSRBulbophyllumOrchidaceaeBiology (General)QH301-705.5BotanyQK1-989ENPlant Diversity, Vol 43, Iss 5, Pp 350-361 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Chloroplast genome Sequence divergence DNA markers SSR Bulbophyllum Orchidaceae Biology (General) QH301-705.5 Botany QK1-989
spellingShingle	Chloroplast genome Sequence divergence DNA markers SSR Bulbophyllum Orchidaceae Biology (General) QH301-705.5 Botany QK1-989 Hanqing Tang Lu Tang Shicheng Shao Yulan Peng Lu Li Yan Luo Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
description	Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.
format	article
author	Hanqing Tang Lu Tang Shicheng Shao Yulan Peng Lu Li Yan Luo
author_facet	Hanqing Tang Lu Tang Shicheng Shao Yulan Peng Lu Li Yan Luo
author_sort	Hanqing Tang
title	Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
title_short	Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
title_full	Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
title_fullStr	Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
title_full_unstemmed	Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution
title_sort	chloroplast genomic diversity in bulbophyllum section macrocaulia (orchidaceae, epidendroideae, malaxideae): insights into species divergence and adaptive evolution
publisher	KeAi Communications Co., Ltd.
publishDate	2021
url	https://doaj.org/article/2cb0378b6426430db05913e6072fb157
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Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

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