An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression

The New World allopolyploid (AD-genome) cottons (Gossypium) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Africa-Asia (the A-genome) and the American tropics and subtropics (the D-genome). Phylogenetic analysis of sequence data from the ribosomal DNA internal transcribed spacer region (ITS1, 5.8S rRNA, ITS2) reveals two strongly supported clades, one corresponding to African species and the other containing all American D-genome species except Gossypium gossypioides, which occupies a basal position within the African clade. This placement conflicts with evidence from fertility relationships, morphology, cytogenetics allozymes, and cpDNA restriction site analysis, which specify a sister-species relationship for G. gossypioides and Gossypium raimondii, deeply embedded within the American D-genome clade. Several alternative explanations for this striking incongruence are considered. The most probable involves: (1) an ancient hybridization event, whereby G. gossypioides experienced contact with an A-genome, either at the diploid level or at the triploid level as a consequence of hybridization with a New World allopolyploid and (2) repeated backcrossing of the hybrid into the G. gossypioides lineage, thereby restoring a nearly pure D-genome, but in the process generating a recombinant ribosomal DNA. We suggest that this process may implicate G. gossypioides, rather than G. raimondii, as the closest living descendant of the ancestral D-genome parent of the allopolyploids. In addition, this example of cryptic, intergenomic introgression between species groups now occupying different hemispheres illustrates how ITS data may provide insights into genome composition and evolutionary history, especially when used in the context of a holistic view that encompasses information from a variety of sources.