Phylogeny of the D-genome
The American diploid species of Gossypium form collectively the subgenus Houzingenia. This taxonomic group includes 13 species (i.e.: G. aridum, G. armourianum, G. davidsonii, G. gossypioides, G. harknessii, G. klotzschianum, G. laxum, G. lobatum, G. raimondii, G. schwendimanii, G. thurberi, G. trilobum, and G. turneri) arranged in two sections and six subsections (sect. Houzingenia, which includes subsect. Houzingenia, subsect. Caducibracteolata, and subsect. Integrifolia; and sect. Erioxylum, which includes subsect. Erioxylum, subsect. Austroamericana, and subsect. Selera). Their taxonomy is well understood, and all of them belong to the same genome group, the so called “D” group (Endrizzi et al., 1985). Several phylogenetic analyses have already been conducted (Cronn et al., 1996; Seelanan et al., 1997; Small & Wendel, 2000; Wendel & Albert, 1992; Wendel et al., 1995) providing support for most of the recognized subsections. However, phylogenetic relationships among the subsections still remain unclear.
To address this question we are using sequences of three independent nuclear genes (A1341, AdhC, and CesA1b) from a total of 33 individuals representing all the 13 D-genome species plus 6 species as outgroup, including 4 Gossypium species from other genomic groups and two species from other genera closely related to Gossypium (Gossypioides and Kokia). The selection of the three genes was made based on the successful results obtained using these genes in previous phylogenetic analyses conducted in other species of Gossypium (Cronn et al., 2002). The amplification and sequencing reactions were made using the primers and PCR conditions described by Cronn et al. (2002).
At the present, we have obtained 95% of the sequences. The most variable of the three markers is the AdhC, followed by the CesA1b, and finally the A1341. There are no incongruences so far among datasets and the preliminary phylogenetic analyses seems very promising.