The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing  

作　　者：Shaohua Xu Ziwen He Zhang Zhang Zixiao Guo Wuxia Guo Haomin Lyu Jianfang Li Ming Yang Zhenglin Du Yelin Huang Renchao Zhou Cairong Zhong David E. Boufford Manuel Lerdau Chung-I Wu Norman C. Duke Suhua Shi 

机构地区：[1]State Key Laboratory of Biocontrol,Guangdong Provincial Key Laboratory of Plant Resources,Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes,School of Life Sciences,Sun Yat-Sen University,Guangzhou 510275,China [2]Core Genomic Facility,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China [3]Hainan Dongzhai Harbor National Nature Reserve,Haikou 571129,China [4]Harvard University Herbaria,Cambridge,MA 02138,USA [5]Departments of Environmental Sciences and of Biology,University of Virginia,Charlottesville,VA 22904-4123,USA [6]Department of Ecology and Evolution,University of Chicago,Chicago,IL 60637,USA [7]Centre for Tropical Water and Aquatic Ecosystem Research,James Cook University,Townsville,QLD 4815,Australia

出　　处：《National Science Review》2017年第5期721-734,共14页国家科学评论（英文版）

基　　金：supported by the National Natural Science Foundation of China(91331202,41130208 and 31600182);the 985 Project(33000–18821105);the National Postdoctoral Program for Innovative Talents(BX201700300);the National Key Research and Development Plan(2017FY100705);the China Postdoctoral Science Foundation(2014M552264 and 2015T80931);the Fundamental Research Funds for the Central Universities(17lgpy99);the Chang Hungta Science Foundation of Sun Yat-Sen University

摘　　要：Mangroves invade some very marginal habitats for woody plants—at the interface between land and sea.Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid(AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits(vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.Mangroves invade some very marginal habitats for woody plants--at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ＂-70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid （AA） usage as well as unusualAA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves＇ highly specialized traits （vivipary and red bark） thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.

关 键 词：MANGROVE whole-genome sequencing adaptive evolution protein evolution genetic diversity sea-level changes 

分 类 号：Q943.2[生物学—植物学]