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

Xu, Shaohua, He, Ziwen, Zhang, Zhang, Guo, Zixiao, Guo, Wuxia, Lyu, Haomin, Li, Jianfang, Yang, Ming, Du, Zhenglin, Huang, Yelin, Zhou, Renchao, Zhong, Cairong, Boufford, David E., Lerdau, Manuel, Wu, Chung-I, Duke, Norman C., The International Mangrove Consortiom, , and Shi, Suhua (2017) The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. National Science Review, 4 (5). pp. 721-734.

[img] PDF (Published Version) - Published Version
Restricted to Repository staff only

View at Publisher Website: http://dx.doi.org/10.1093/nsr/nwx065
 
22
1


Abstract

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 13.3Mb, 5.4Mb and 1.0Mb, 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 similar to 70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exomemodifications 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.

Item ID: 51952
Item Type: Article (Research - C1)
ISSN: 2053-714X
Keywords: mangrove, whole-genome sequencing, adaptive evolution, protein evolution, genetic diversity, sea-level changes
Funders: National Natural Science Foundation of China (NNSF), The 985 Project (T985P), National Key Research and Development Plan of China (NKRDP), China Postdoctoral Science Foundation (CPDSF), National Postdoctoral Program for Innovative Talents (NPPIT), Fundamental Research Funds for the Central Universities of China (FRFCU), Chang Hungta Science Foundation (CHSF)
Projects and Grants: NNSF 91331202, NNSF 41130208, NNSF 31600182, T985P 33000-18821105, NPPIT BX201700300, NKRDP 2017FY100705, CPDSF 2014M552264, CPDSF 2015T80931, FRFCU 17lgpy99
Date Deposited: 10 Jan 2018 07:48
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060407 Genome Structure and Regulation @ 40%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 30%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 30%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960802 Coastal and Estuarine Flora, Fauna and Biodiversity @ 40%
96 ENVIRONMENT > 9613 Remnant Vegetation and Protected Conservation Areas > 961304 Remnant Vegetation and Protected Conservation Areas in Coastal and Estuarine Environments @ 40%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 20%
Downloads: Total: 1
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page