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

Yaodong Yang,Stéphanie Bocs,Junyang Xu,Chantal Hamelin,Amjad Iqbal,Ming Peng,Rashad Qadri,Wei Xia,Alix Armero,Lixia Zhou,Zhiying Ma ,Hang Fan ,Na Liu,Ronan Rivallan,Yi Wu,Jing Li,Dominique This,Pengwei Xu,Auguste Emmanuel Issali,Luc Baudouin,Yong Xiao

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.

Highlights

1234567890():,; Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe
In order to assign the coconut sequences to their positions on coconut chromosomes, we created a linkage map, based on a back-cross MYD × (MYD × WAT) produced and planted in Côte d’Ivoire (WAT stands for the West African Tall and MYD for the Malayan Yellow Dwarf)
After DNA extraction, a legitimacy test involving fifteen microsatellite markers was performed on 320 progenies and confirmed the origin of 292 progenies, which were genotyped by genotyping by sequencing (GBS), along with the parents

Summary

Introduction

1234567890():,; Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. Coconut (Cocos nucifera L.) is a continuously fruiting evergreen perennial tropical monocotyledon, adapted to humid and sub-humid coastal environments. Because of its importance in sustaining the life of coconut growers and its various economic uses, coconut is often regarded as a “tree of life” It is grown in more than 92 countries, covers 12.2 million ha of plantation area, of which 85% is found in the Asia-Pacific region. Coconut is naturally adapted to the coastal environment and, as a facultative halophyte, is tolerant to variable levels of water salinity. In Cl-deficient soils, salt can be used as fertilizer, and a

Methods

Results

Conclusion