Mining SSR and SNP/Indel sites in expressed sequence tag libraries of Radopholus similis

Abstract

The objective of this study is to explore the single sequence repeats (SSRs) and single nucleotide polymorphims (SNPs) in expressed sequence tags (ESTs) of Radopholus similis. We retrieved 7380 EST sequences consisting different tissues/condition libraries from dbEST of National Centre for Biotechnology Information (NCBI). A total of 1449 SSRs were detected by MISA perl script. Hexa-nucleotide repeats (836 nos.) followed by mononucleotide repeats (207 nos.) were found to be more abundant than other types of repeats. Putative SNP/Indels were found out with the help of AutoSNP. As many as 1038 SNPs and 108 small indels (insertion/deletion) were found with a density of one SNP/191 bp and one indel/1.8 kbp. Candidate SNPs were categorized according to nucleotide substitution as either transition (C↔T or G↔A) or transversion (C↔G, A↔T, C↔A or T↔G). We observed a higher number of transversions type substitution (537) than transitions (501). However considering the individual substitutions, G↔A (281) and C↔T (220) were found to be predominant than purine to pyrimidine base substitutions. Since the SSR and SNP markers are invaluable tools for genetic analysis, the identified SSRs and SNPs of R. similis could be used in diversity analysis, genetic trait mapping, association studies and marker assisted selection.