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

The FAD2-1 microsomal omega-6 desaturase gene contains a large intron (apprx1133 bp (base pairs)) in the 5' 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.