Convergent adaptation of the genomes of woody plants at the land-sea interface

He, Ziwen, Xu, Shaohua, Zhang, Zhang, Guo, Wuxia, Lyu, Haomin, Zhong, Cairong, Boufford, David E., Duke, Norman C., The International Mangrove Consortium, , and Shi, Suhua (2020) Convergent adaptation of the genomes of woody plants at the land-sea interface. National Science Review, 7 (6). pp. 978-993.

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Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P-true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

Item ID: 63776
Item Type: Article (Research - C1)
ISSN: 2053-714X
Keywords: convergent evolution, genome, mangrove, adaptive evolution, woody plants
Copyright Information: © The Author(s) 2020. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Funders: National Natural Science Foundation of China (NNSFC), National Key Research and Development Plan of China (NKRDP), Guangdong Basic and Applied Basic Research Foundation (GBABRF), China Postdoctoral Science Foundation (CPDSF), National Postdoctoral Program for Innovative Talents (NPPIT)
Projects and Grants: NNSFC 31830005, NNSFC 91731301, NNSFC 31971540, NKRDP 2017FY100705, GBABRF 2019A1515010752, CPDSF 2017M622857, NPPIT BX201700300
Date Deposited: 15 Jul 2020 07:43
FoR Codes: 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310404 Evolution of developmental systems @ 50%
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310402 Biogeography and phylogeography @ 40%
41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410401 Conservation and biodiversity @ 10%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960802 Coastal and Estuarine Flora, Fauna and Biodiversity @ 50%
97 EXPANDING KNOWLEDGE > 970105 Expanding Knowledge in the Environmental Sciences @ 50%
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