期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2022
卷号：119
期号：39
DOI：10.1073/pnas.2208496119
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance
Wild relatives of domesticated plants provide a rich resource for crop improvement and a valuable comparative perspective for understanding genomic, physiological, and agricultural traits. Here, we provide high-quality reference genomes of one early domesticated form of the economically most important cotton species,
Gossypium hirsutum, and two other wild species, to clarify evolutionary relationships and understand the genomic changes that characterize these species and their close relatives. We document abundant gene resources involved in adaptation to environmental challenges, highlighting the potential for introgression of favorable genes into domesticated cotton and for increasing resilience to climate variability. Our study complements other recent genomic analyses in the cotton genus and provides a valuable foundation for breeding improved cotton varieties.
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.
