摘要Due to the economic value of natural textile fiber,cotton has attracted much research attention,which has led to the publication of two diploid genomes and two tetraploid genomes.These big data facilitate functional genomic study in cotton,and allow researchers to investigate cotton genome structure,gene expression,and protein function on the global scale using high-throughput methods.In this review,we summarized recent studies of cotton genomes.Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution.Alternative splicing of cotton transcriptomes was evaluated genome-widely.Several important gene families like MYC,NAG Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function.High-throughput proteomics also unraveled the key functional proteins correlated with fiber development.Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.