Evolution of the FAD2-1 fatty acid desaturase 5 UTR intron and the molecular systematics of Gossypium (Malvaceae)

The FAD2-1 microsomal -6 desaturase gene contains a large intron (~1133 bp [base pairs]) in the 5ʹ untranslated region that may participate in gene regulation and, in Gossypium, is evolving at an evolutionary rate useful for elucidating recently diverged lineages. FAD2-1 is single copy in diploid Gossypium species, and two orthologs are present in the allotetraploid species. Among the diploid species, the D-genome FAD2-1 introns have accumulated substitutions 1.4–1.8 times faster than the A-genome introns. In the tetraploids, the difference between the D-subgenome introns and their A-subgenome orthologs is even greater. The substitution rate of the intron in the D-genome diploid G. gossypioides more closely approximates that of the A genome than other D genome species, highlighting its unique evolutionary history. However, phylogenetic analyses support G. raimondii as the closest living relative of the D-subgenome donor. The Australian K-genome species diverged 8–16 million years ago into two clades. One clade comprises the sporadically distributed, erect to suberect coastal species; a second clade comprises the more widely spread, prostrate, inland species. A comparison of published gene trees to the FAD2-1 intron topology suggests that G. bickii arose from an early divergence, but that it carries a G. australe-like rDNA captured via a previously undetected hybridization event.