Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Abstract

Allotetraploid cotton ( Gossypium ) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD) 6 , Ge ] and Gossypium stephensii [(AD) 7 , Gs ], and one early form of domesticated Gossypium hirsutum , race punctatum [(AD) 1 , Ghp ]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs , Ge , and domesticated G. hirsutum . We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance

“…Cotton is a vital source of natural fiber crops in the world and one of the main sources of plant protein and plant oil, and it is one of the important strategic materials in China ( Liu et al., 2022 ). Around 1.6 million years ago, the A 0 -genome of an extinct diploid cotton and the D 5 -genome of the diploid cotton Gossypium raimondiid were crossed and doubled to form a heterotetraploid species ( Grover et al., 2015 ; Huang et al., 2020 ; Peng et al., 2022 ). This tetraploid specie then diverged subsequently into seven tetraploid cottons namely G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum , G. darwinii , G. ekmanianum , and G. stephensii , and the genomes of these seven tetraploid cotton species were labeled as (AD) 1 to (AD) 7 ( Chen et al., 2020b ; Peng et al., 2022 ).…”

“…Around 1.6 million years ago, the A 0 -genome of an extinct diploid cotton and the D 5 -genome of the diploid cotton Gossypium raimondiid were crossed and doubled to form a heterotetraploid species ( Grover et al., 2015 ; Huang et al., 2020 ; Peng et al., 2022 ). This tetraploid specie then diverged subsequently into seven tetraploid cottons namely G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum , G. darwinii , G. ekmanianum , and G. stephensii , and the genomes of these seven tetraploid cotton species were labeled as (AD) 1 to (AD) 7 ( Chen et al., 2020b ; Peng et al., 2022 ). Among them, G. hirsutum and G. barbadense were domesticated as cultivated species, the two cultivated allotetraploid cotton species with quite different traits in morphology, yield, fiber quality, environmental adaptability, and genomic sequences ( Hu et al., 2019 ).…”

Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses

“…In addition, positive selection is associated with shifts in function and the environment (Hu et al, 2014;Li et al, 2018). Thus, the sites under positive selection determined in this study might drive the changes in PCGs, allowing adaptation to diverse and harsh habitats (Li et al, 2018;Dhar et al, 2020;Peng et al, 2022).…”

Recent progression and future perspectives in cotton genomic breeding

“…The assembly length of the latest version of the G. babardense genome is 2,210 Mb with a contig N50 of 9.24 Mb (Ma et al, 2021b). Genomes for G. anomalum (B 1 ) (Grover et al, 2021a; Xu et al, 2022), G. australe (G 2 ) (Cai et al, 2020), G. bickii (G 1 ) (Sheng et al, 2022), G. ekmanianum and G. stephensill (Peng et al, 2022), G. rotundifolium (K 2 ) (Wang et al, 2021b), and G. stocksii (E 1 ) (Grover et al, 2021b), were also sequenced and successfully assembled. These cotton genome sequences have the potential to provide powerful genomic markers and target genes for genomic selection in cotton.…”