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

doi:10.1016/j.pld.2021.01.003

Plant Diversity ›› 2021, Vol. 43 ›› Issue (05): 350-361.DOI: 10.1016/j.pld.2021.01.003

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

Hanqing Tang^a, Lu Tang^a,b, Shicheng Shao^a, Yulan Peng^c, Lu Li^d, Yan Luo^a,e

a Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China;
b College of Forestry, Shanxi Agricultural University, Taigu, Jinzhong, 030800, Shanxi, China;
c Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China;
d Department of Biodiversity Conservation, Southwest Forestry University, Kunming, 650224, Yunnan, China;
e Gardening and Horticulture Department, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China

收稿日期:2020-10-29 修回日期:2021-01-07 出版日期:2021-10-25 发布日期:2021-11-18
通讯作者: Lu Li, Yan Luo
基金资助:
We are grateful to Wenbin Yu, Yu Song, from Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Fei Zhao from Kunming Institute of Botany, Chinese Academy of Sciences, for their help in genomic data analysis. We also thank Lin Li, from South China Botanical Garden, Chinese Academy of Sciences, Xiaoyun Wang and Zhifeng Xu from the Orchid Conservation Center of Yunnan Fengchunfang Biotechnology Co., Ltd, for kindly providing photos and sample materials. This work was supported by the National Natural Science Foundation of China (No. 31870183, No.U1702235) and Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (Y4ZK111B01).

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

Hanqing Tang^a, Lu Tang^a,b, Shicheng Shao^a, Yulan Peng^c, Lu Li^d, Yan Luo^a,e

a Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China;
b College of Forestry, Shanxi Agricultural University, Taigu, Jinzhong, 030800, Shanxi, China;
c Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China;
d Department of Biodiversity Conservation, Southwest Forestry University, Kunming, 650224, Yunnan, China;
e Gardening and Horticulture Department, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China

Received:2020-10-29 Revised:2021-01-07 Online:2021-10-25 Published:2021-11-18
Contact: Lu Li, Yan Luo
Supported by:
We are grateful to Wenbin Yu, Yu Song, from Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Fei Zhao from Kunming Institute of Botany, Chinese Academy of Sciences, for their help in genomic data analysis. We also thank Lin Li, from South China Botanical Garden, Chinese Academy of Sciences, Xiaoyun Wang and Zhifeng Xu from the Orchid Conservation Center of Yunnan Fengchunfang Biotechnology Co., Ltd, for kindly providing photos and sample materials. This work was supported by the National Natural Science Foundation of China (No. 31870183, No.U1702235) and Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (Y4ZK111B01).

摘要/Abstract

摘要： 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.

关键词: Chloroplast genome, Sequence divergence, DNA markers, SSR, Bulbophyllum, Orchidaceae

Abstract: 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.

Key words: Chloroplast genome, Sequence divergence, DNA markers, SSR, Bulbophyllum, Orchidaceae

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[J]. Plant Diversity, 2021, 43(05): 350-361.

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

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

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