Variations in New World Tetraploid Cotton Genomes, Suvin and BCS-23 Reveal Unique Alleles

Polyploid (tetraploid) cotton genomes are high yielding and exhibit high quality fibre compared to diploid genomes. We have sequenced two tetraploid cotton, G.barbadense (AD2) genomes, Suvin and BCS 23-18-7 along with two diploid cotton genomes, G.herbaceum (Jayadhar) and G.arboreum (DLSA) for comparison. Paired-end (100bp) data was generated for Suvin and BCS23-18-7 respectively on Illumina HiSeq 2500, next generation sequencing platform. In order to obtain high quality data, the raw data was subjected to adapter trimming and base quality trimming. The data was used for generating denovo assemblies and compared with tetraploid genomes G.hirsutum and G.barbadense genomes. The assemblies were used to understand the synteny between genomes. Further, the data was mapped to G.barbadense and G.hirsutum genomes and variation analysis performed to discover polymorphic and unique alleles in Suvin and BCS 23-18-7. The variation data could further be used to aid association studies on fibre quality and development.