Exploiting the Great Potential of Sequence Capture Data By a New Tool, SUPER-CAP

The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of target regions. However, the association of the genomic variation with certain traits requires a reliable detection and a systematic investigation of the entire spectrum of DNA variation, including single nucleotide polymorphisms, insertions/deletions as well as copy number variation (CNV), and presence/absence variation (PAV). In this study, we present SUPER-CAP (Ruggieri et al., 2016), a bioinformatics web tool aimed at handling Sequence Capture data. The tool, profiting by SUPER-W (Sanseverino et al, 2015), was developed to handle Sequence Capture data, fine calculate the allele frequency of variations and to build private sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40#) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.