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01 22, 2021;4 (1): 105.

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

Yaodong Yang, Stéphanie Bocs, Haikuo Fan, Alix Armero, Luc Baudouin, Pengwei Xu, Junyang Xu, Dominique This, Chantal Hamelin, Amjad Iqbal, Rashad Qadri, Lixia Zhou, Jing Li, Yi Wu, Zilong Ma, Auguste Emmanuel Issali, Ronan Rivallan, Na Liu, Wei Xia, Ming Peng, Yong Xiao
Author Information
  1. Yaodong Yang: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China. ORCID
  2. Stéphanie Bocs: CIRAD, UMR AGAP, F-34398, Montpellier, France. ORCID
  3. Haikuo Fan: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
  4. Alix Armero: AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.
  5. Luc Baudouin: CIRAD, UMR AGAP, F-34398, Montpellier, France. luc.baudouin@cirad.fr. ORCID
  6. Pengwei Xu: BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China.
  7. Junyang Xu: BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China.
  8. Dominique This: AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France. ORCID
  9. Chantal Hamelin: CIRAD, UMR AGAP, F-34398, Montpellier, France.
  10. Amjad Iqbal: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China. ORCID
  11. Rashad Qadri: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
  12. Lixia Zhou: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
  13. Jing Li: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
  14. Yi Wu: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
  15. Zilong Ma: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China.
  16. Auguste Emmanuel Issali: Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA)07 B.P. 13, Port Bouet, Côte d'Ivoire.
  17. Ronan Rivallan: CIRAD, UMR AGAP, F-34398, Montpellier, France.
  18. Na Liu: BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China.
  19. Wei Xia: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China. saizjxiawei@hainu.edu.cn. ORCID
  20. Ming Peng: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China. pengming@itbb.org.cn. ORCID
  21. Yong Xiao: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China. xiaoyong1980@catas.cn. ORCID
PMID: 33483627 DOI: 10.1038/s42003-020-01593-x

Abstract

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.

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MeSH Term

Biological Evolution
Chromosome Mapping
Chromosomes, Plant
Cocos
DNA Transposable Elements
Genome, Plant
Genotyping Techniques
Reference Standards
Salt Tolerance
Signal Transduction

Chemicals

DNA Transposable Elements
Journal Article Research Support, Non-U.S. Gov't

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