High quality SNPs/Indels mining and characterization in ginger from ESTs data base

Ginger (Zingiber officinale Rosc.) is an important herb of the family Zingiberaceae. It is accepted as a universal cure for a multitudeof diseases in Indian systems of medicine and its rhizomes are equally popular as a spice ingredient throughout Asia. SNPs, thedefinitive genetic markers, representing the finest resolution of a DNA sequence, are abundantly found in populations having alower rate of mutation and are used for genomic analysis. The public ESTs sequences mostly lack quality files, making high qualitySNPs detection more difficult since it is exclusively based on sequence comparisons. In the present study, current dbESTs of NCBIwas mined and 38115 ginger ESTs sequences were obtained and assembled into contigs using CAP3 program. In this analysis,recent software tool QualitySNP was used to detect 11523 potential SNPs sites, 8810 high quality SNPs and 1008 indelspolymorphisms with a frequency of 1.61 SNPs / 10 kbp. Of ESTs libraries generated from three ginger tissues together, rhizomeshad a frequency of 0.32 SNPs and 0.03 indels per 10 kbp whereas the leaves had a frequency of 2.51 SNPs and 0.23 indels per 10kbp and root is showing relative frequency of 0.76/10 kbp SNPs and 0.02/10 kbp indels. The present analysis provides additionalinformation about the tissue wise presence of haplotypes (222), distribution of high quality exonic (2355) and intronic (6455) SNPsand information about singletons (7538) in addition to contigs transitions and transversions ratio (0.57). Among all tissue detectedSNPs, transversions number is higher in comparison to the number of transitions. Quality SNPs detected in this work can be usedas markers for further ginger genetic experiments.