Comparative genomics analyses reveal genomic variation and evolutionary adaptation in Dendrobium orchids
Bing-Jie Chen, Jieyu Wang, Shan-Ce Niu, Qi-Hang Chen, Xiaofang Chen, Pei‐Ji Zheng, Yu-Min Liang, Kang‐Li Li, Zhang-Zhen Zheng, Yingyi Liang, Cuili Zhang, Xuewei Zhao, Jun Li, Xin He, Linying Wang, Ye Huang, Qinyao Zheng, Mengmeng Zhang, Deqiang Chen, Cheng‐Yuan Zhou, Meng-Yao Zeng, Zhuang Zhou, Ming‐Zhong Huang, Zhuang Zhao, Donghui Peng, Zihao He, Long−Hai Zou, Baocai Han, Wen‐Chieh Tsai, Siren Lan, Guoqiang Zhang, Zhong‐Jian Liu, Qing Xu
Abstract
The mechanisms of species formation and diversity within the Orchidaceae have always been a topic of great research interest, and molecular biology-based explanations for these phenomena are lacking. Here, we present a comparative genomic analysis comprising 24 chromosome-level genome assemblies and genome skimming data for 204 species from Dendrobium. We identify that the genetic conservation in Dendrobium is associated with its environmental adaptability. And the formation of species diversity in the genus Dendrobium is driven by the compression of the Indian plate and changes in sea level and precipitation. The CYP734A50 might play important role in Dendrobium self-incompatibility (SI) species and the type-1 SI system lost through deletion of the entire single polymorphic locus (S-locus). Our results reveal the genetics background of genomic variation, biosynthesis, and adaptive evolution in Dendrobium, providing fundamental insights into the relationships between the genome and trait evolution of orchids and into angiosperm diversification. Dendrobium is a genus of mostly epiphytic and lithophytic orchids. Here, the authors conduct comparative genome analysis for 24 chromosome-level genome assemblies and genome skimming sequencing data for 204 species in this genus, and reveal genomic variation, biosynthesis and evolutionary adaptation in Dendrobium orchids.