Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Z Jeffrey Chen ,Daniel G Peterson,Jerry Jenkins,David M Stelly,Luis De Santiago ,Don C Jones,Guanjing Hu,Jonathan F Wendel,Amanda M Hulse‐Kemp ,Bo Liu,Ryan C Kirkbride,Christopher Saski ,Joseph W Carlson,Mingquan Ding,Qingxin Song,Atsumi Ando,Li Wen,Shengqiang Shu,Justin L Conover,Corrinne E Grover,Sheron A Simpson ,Brian E Scheffler,John T Lovell ,Avinash Sreedasyam,Melissa E Williams ,Robert N Vaughn ,Keith Mcgee,Yu-Ming Lin,Wenxue Ye,Lori Beth Boston ,Christopher Plott,Jane Grimwood,Jeremy Schmutz

doi:10.1038/s41588-020-0614-5

Abstract

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

Highlights

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive
We analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. These polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages
The assembled genomes range in size from 2.2 to 2.3 gigabase pairs (Gbp; Table 1), slightly smaller than the sum of the two A- and D-genome diploids (1.7/A + 0.8/D ≈ 2.5 Gbp/AD)[20,21]

Summary

Introduction

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. We analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons These polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. Polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement. Future improvements in cotton and sustainability will involve use of the genomic resources and gene-editing tools becoming available in many crops[9,18,19] These analyses have shown structural, genetic and gene expression variation related to fiber traits and stress responses in cultivated.

Methods

Results

Conclusion