Whole Genome Sequencing and Analysis of the 'A' Genome of Indian Diploid Cottons Gossypium arboreum and Gossypium herbaceum

Draft genome sequence of 'D5' genome (Wang et al. 2012) and 'A' genome (Li et al., 2014) is paving the path for understanding the tetraploid genomes of cotton. Application of these genomic resources requires a systemic understanding of 'A' genome for mapping complex traits in tetraploid cotton with GWAS approach. Here we report sequencing and analysis of two diploid cotton species with 'A' genome, Gossypium arboreum cv DLSA (GarDLS) with A2 genome (ca. 1.75 Gb) and Gossypium herbaceum cv Jayadhar (GheJay) with A1 genome (ca. 1.5 Gb).  A total of 96 Gb, 132 Gb of clean sequence covering the genome by 67 and 80 fold was obtained by paired-end sequencing for GarDLS and GheJay respectively. We further anchored 90% of the assembly on 13 pseudochromosomes forming 1.35Gb and 1.37 Gb pseudomolecules with 36 Mb and 194 Mb unaligned scaffolds for GarDLS and GheJay respectively. Variant calling between GarDLS & G.raimondii was performed which has shown 11.55 million variants which is useful for discrimination of  intragenomic variants in G.hirsutum breeding. Similarly, a total of 12.24 million variants are identified between GheJay and G.raimondii which are useful in G. barbadense breeding. Comparison of G. arboreum cv SXY1 and GarDLS revealed 4.14 million SNPs and G.arboreum cv SXY1 & GheJay revealed 14.23 miilion SNPs and 5.02 million indels. A total of 19.76 variants are observed between GarDLS & GheJay which are expected to serve as rich resource for mapping commercially important traits such as fibre quality and lint yield and their cotton productivity.