Genome Resquencing of Select Cotton Diploid Accessions

There are two distinct classes of SNPs in allotetraploid cotton: SNPs between alleles (allele-SNPs) and SNPs between the A and D genomes (homoeo-SNPs). Discrimination between these two types of SNPs has been a major obstacle for cotton improvement programs, which rely on molecular markers. In order to provide valuable resources for these programs, we resequenced the genomes of 5 A-genome and 5 D-genome diploid cotton accessions. By aligning these reads to the completed D₅ reference genome sequence, we identified a robust set of homoeo-SNPs between the A- and D-genomes. Because of the relatively recent divergence of the A_T- and D_T-genomes from their diploid relatives, homoeo-SNPs between extant diploids are a reasonable approximation of homoeo-SNPs between the A_T- and D_T- genomes of allotetraploid cotton. We filtered out these homoeo-SNPs to accurately identify allele-SNPs within and between cotton accessions. In addition to providing information on specific SNPs, this collection of homoeo- and allele-SNPs will allow researchers to 1) reduce the bias in mapping efficiency between sequence reads originating from the A_T- and D_T-genomes, 2) identify the genomic origin of sequence reads from allotetraploid cotton, and 3) discriminate or ignore homoeo-SNPs during sequence analysis of allotetraploid cotton (e.g. marker development, GBS, RNA-seq, ChIP-seq, MethylC-seq, etc.)