Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

Upon assembling the first Gossypium herbaceum (A(1)) genome and substantially improving the existing Gossypium arboreum (A(2)) and Gossypium hirsutum ((AD)(1)) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A(0), which was more phylogenetically related to A(1) than A(2). Further, allotetraploid formation was shown to have preceded the speciation of A(1) and A(2). Both A-genomes evolved independently, with no ancestor–progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)(1). Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement.