Transcriptome Assembly, Annotation and Molecular Marker Discovery of Capsicum Annuum Varieties Mandarin and Blackcluster

Next generation sequencing technologies are rapid, cost-effective means for assembly and characterization of gene content and identification of molecular markers. High-throughput transcriptome profiling of two pepper (Capsicum annuum L., Solanaceae) cultivars, Mandarin and Blackcluster, was performed using 454 GS-FLX pyrosequencing. 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54 Mb of sequence data resulted from 17,525 and 16,341 ‘isogroups’ and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the varieties, respectively. Functional annotation of the assembled sequences was done based on homology to genes in multiple public databases. A total of 9,701 and 12,741 potential SNPs were indentified for both cultivars, which eventually resulted in 1,025 and 1,059 genotype specific SNPs, for both the varieties, respectively. These studies for pepper will be highly valuable for marker-assisted breeding and other detailed genetic studies.  

Keywords: Transcriptome assembly, Capsicum annuum, SNPs, Molecular markers