Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome

• Two cotton subgenomes (At and Dt) do not contribute equally to fiber development.
• Dt subgenome provides many fiber genes upon its merger with the At subgenome.
• At subgenome has greater similarity of fiber genes with the wild D genome than Dt.
• The findings provide insights into the evolution and the distribution of fiber genes.
• Exploitation of the fiber genes allows for accelerated and efficient cotton breeding.

Cotton fiber represents the largest single cell in plants and they serve as models to study cell development. This study investigated the distribution and evolution of fiber Unigenes anchored to recombination hotspots between tetraploid cotton (Gossypium hirsutum) At and Dt subgenomes, and within a parental diploid cotton (Gossypium raimondii) D genome. Comparative analysis of At vs D and Dt vs D showed that 1) the D genome provides many fiber genes after its merger with another parental diploid cotton (Gossypium arboreum) A genome although the D genome itself does not produce any spinnable fiber; 2) similarity of fiber genes is higher between At vs D than between Dt vs D genomic hotspots. This is the first report that fiber genes have higher similarity between At and D than between Dt and D. The finding provides new insights into cotton genomic regions that would facilitate genetic improvement of natural fiber properties.