Data from: Types, levels, and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

To explore types, levels, and patterns of genetic divergence among diploid
Gossypium (cotton) genomes, 780 cDNA, genomic DNA, and SSR loci were
re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G.
raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup,
Gossypioides kirkii. Divergence among these genomes ranged from 7.32
polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to
only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are
least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic
sites per 100 base pairs, while ESTs are most conserved with 3.96
polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest
percentage of 'extended polymorphisms' (spanning multiple
consecutive nucleotides). The A genome lineage was particularly rapidly
evolving, with the D genome also showing accelerated evolution relative to
the C genome. Unexpected asymmetry in mutation rates was found, with much
more transition than transversion mutation in the D genome after its
divergence from a common ancestor shared with the A genome. This large
quantity of orthologous DNA sequence strongly supports a phylogeny in
which A-C divergence is more recent than A-D divergence, a subject that is
of much importance in view of A-D polyploid formation being key to the
evolution of the most productive and finest-quality cottons. Loci that are
monomorphic within A or D genome types, but polymorphic between genome
types, may be of practical importance for identifying locus-specific DNA
markers in tetraploid cottons including leading cultivars.