Towards Integrative Cyto-Genomics of the c12/c26 Homeologous Chromosome Pair of Cotton

Several groups worldwide are working toward whole-genome sequencing of upland cotton (Gossypium hirsutum (L.). The task is a formidable one, in that while upland cotton is regarded widely as tetraploid (2n = 4x = 52), it and other AD-genome Gossypium species are actually partially diploidized and also paleopolyploid; they have accordingly complex genomes. A high quality sequence assembly was published in 2012 for the D5 genome (n=13) and this serves as an immensely valuable, albeit imperfect, reference genome. The D5 genome is from a wild Peruvian relative of cotton, Gossypium raimondii, which is generally considered to be the most closely related 13-chromosome genome to the D subgenome of upland cotton. Once sequencing assemblies are completed and published, it will be highly desirable to integrate various kinds of maps, sequence contigs and scaffolds to cytogenetic maps of chromosomes. Toward that end, we have started developing BAC-FISH-based cytological maps of the upland cotton genome. The initial results with a pair of homeologous chromosomes, 12 and 26 from the A and D subgenomes, respectively, provide a genomic sample to begin characterizing genome organization, A-D differences and genome evolution.