Authors: V. Ruggieri, I. Anzar, A. Paytuvi, R. Calafiore, R. Aiese Cigliano, W. Sanseverino, A. Barone
Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
Sequentia Biotech SL, Calle Comte d’Urgell, 240, 08035 Barcelona, Spain
Publication: DNA Research
Date: December 2016
The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific 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.