Localization of high level of sequence conservation and divergence regions in cotton

In a previous study, we observed that the variations in chromosome size are due to uneven expansion and contraction by comparing the structures and sizes of a pair of homoeologous high-resolution cytogenetic maps of chromosomes 12A and 12D in tetraploid cotton. To reveal the variation at the sequence level, in the present paper, we sequenced two pairs of homoeologous bacterial artificial chromosomes derived from high- to low-variable genomic regions. Comparisons of their sequence variations confirmed that the highly conserved and divergent sequences existed in the distal and pericentric regions, e.g., high- and low-variable genome size regions in these two pairs of cotton homoeologous chromosomes. Sequence analysis also confirmed that the differential accumulation of Gossypium retrotransposable gypsy-like element (Gorge3) accounted for the main contributions for the size difference between the pericentric regions. By fluorescence in situ hybridization analysis, we found that Gorge3 has a bias distribution in the A_T/A proximal regions and is associated with the heterochromatin along the chromosomes in the entire Gossypium genome. These results indicate that, between A_T/A and D_T/D genomes, the distal and pericentric regions usually possess high level of sequence conservation and divergence, respectively, in cotton.