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Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance

文献类型： 外文期刊

作者： Yang, Yaodong 1 ; Bocs, Stephanie 2 ; Fan, Haikuo 1 ; Armero, Alix 3 ; Baudouin, Luc 2 ; Xu, Pengwei 5 ; Xu, Junyang 5 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Hainan Key Lab Trop Oil Crops Biol, Coconut Res Inst, Wenchang 571339, Hainan, Peoples R China

2.CIRAD, UMR AGAP, F-34398 Montpellier, France

3.Univ Montpellier, AGAP, CIRAD, INRAE,Inst Agro, F-34398 Montpellier, France

4.IRD, South Green Bioinformat Platform, Biovers, CIRAD,INRAE, F-34398 Montpellier, France

5.BGI Shenzhen, BGI Genom, Shenzhen 518083, Peoples R China

6.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Haikou 571101, Hainan, Peoples R China

7.Ctr Natl Rech Agron CNRA, Stn Cocotier Marc Delorme, 07 BP 13, Port Bouet, Cote Ivoire

期刊名称：COMMUNICATIONS BIOLOGY （ 影响因子：6.268； 五年影响因子：6.268 ）

ISSN：

年卷期： 2021 年 4 卷 1 期

页码：

收录情况： SCI

摘要： Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n=32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community. Yaodong Yang et al. report a chromosome-scale genome assembly of the coconut and transcriptome analysis of coconut leaves. Their analysis reveals important steps along the evolutionary trajectory of palms and identifies genes that may play a key role in tolerance to salt stress.

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