Backbone phylogeny of Salix based on genome skimming data  

作　　者：Kai-Yun Chen Jin-DanWang Rui-Qi Xiang Xue-Dan Yang Quan-Zheng Yun Yuan Huang Hang Sun Jia-Hui Chen 

机构地区：[1]CAS Key Laboratory for Plant Diversity and Biogeography of East Asia,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,Yunnan,PR China [2]University of Chinese Academy of Sciences,Beijing 100049,PR China [3]Beijing Ori-Gene Science and Technology Co Ltd,Beijing 102206,PR China [4]School of Life Sciences,Yunnan Normal University,Kunming 650092,Yunnan,PR China

出　　处：《Plant Diversity》2025年第2期178-188,共11页植物多样性(英文版)

基　　金：supported by NSFC(32070226,32360065);the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149);the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2024QZKK0200);Yunnan Fundamental Research Projects(202101AS070032);the CAS“Light ofWest China”Program(xbzg-zdsys-202110);the Yunnan Innovation Team Project(202305AS350004,with LD/NY/SB/CJG/CJH as the core member).

摘　　要：The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.

关 键 词：SALIX Genome skimming PHYLOGENOMICS Orthologous coding sequencing Subgeneric classification 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]