Bioinformatics for the Comparative Genomic Analysis of the Cotton (Gossypium) Polyploid Complex

摘要: Bioinformatics for the Comparative Genomic Analysis of Cotton (Gossypium) Polyploid Complex Justin Thomas Page Department Biology, BYU Doctor Philosophy Understanding composition, evolution, and function cotton genome is complicated by joint presence two genomes in its nucleus (AT DT genomes). Specifically, read-mapping (a fundamental part next-generation sequence analysis) cannot adequately differentiate reads as belonging to one or other. These were derived from progenitor A-genome D-genome diploids involved ancestral allopolyploidization. To better understand allopolyploid genome, we developed PolyCat categorize according their origin based on homoeo-SNPs that genomes. We re-sequenced extant diploid relatives tetraploid contain A1 (G. herbaceum), A2 arboreum), D5 raimondii) identified 24 million SNPs between A-diploid D-diploid analyses facilitated construction a robust index conserved A-genomes Dgenomes at all detected polymorphic loci. This can be used assign an allotetraploid genome-of-origin. Continued characterization Gossypium will further enhance our ability manipulate fiber agronomic production cotton. With new whole-genome re-sequencing data 34 lines cotton, representing species, explored evolution with greatly improved resolution tools, including BamBam PolyDog. Identifying structural variants among these relatives, clarified phylogenetic relationships newly characterized identify introgression different species cultivated homoeologs ATand DT-genomes especially phenomenon homoeologous conversion. Homoeologous conversion rare perhaps due vast difference chromosome sizes Several regions have been introgressed G. hirsutum barbadense resulting superior cultivars, likely beneficial alleles both novel combinations alleles. The genomic provide valuable resource researchers breeders, who freely access online CottonGen.