Reanalysis of genome sequences of tomato accessions and its wild relatives: development of Tomato Genomic Variation (TGV) database integrating SNPs and INDELs polymorphisms

• Published in: Bioinformatics 2020-12, Vol.36 (20), p.4984-4990
• Main Authors: Gupta, Prateek, Dholaniya, Pankaj Singh, Devulapalli, Sameera, Tawari, Nilesh Ramesh, Sreelakshmi, Yellamaraju, Sharma, Rameshwar
• Format: Article
• Language: English
• Subjects: DNA, Plant; Genome, Plant - genetics; Genomics; Lycopersicon esculentum - genetics; Polymorphism, Single Nucleotide - genetics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btaa617

Abstract Motivation Facilitated by technological advances and expeditious decrease in the sequencing costs, whole-genome sequencing is increasingly implemented to uncover variations in cultivars/accessions of many crop plants. In tomato (Solanum lycopersicum), the availability of the genome sequence, followed by the resequencing of tomato cultivars and its wild relatives, has provided a prodigious resource for the improvement of traits. A high-quality genome resequencing of 84 tomato accessions and wild relatives generated a dataset that can be used as a resource to identify agronomically important alleles across the genome. Converting this dataset into a searchable database, including information about the influence of single-nucleotide polymorphisms (SNPs) on protein function, provides valuable information about the genetic variations. The database will assist in searching for functional variants of a gene for introgression into tomato cultivars. Results A recent release of better-quality tomato genome reference assembly SL3.0, and new annotation ITAG3.2 of SL3.0, dropped 3857 genes, added 4900 novel genes and updated 20 766 genes. Using the above version, we remapped the data from the tomato lines resequenced under the ‘100 tomato genome resequencing project’ on new tomato genome assembly SL3.0 and made an online searchable Tomato Genomic Variations (TGVs) database. The TGV contains information about SNPs and insertion/deletion events and expands it by functional annotation of variants with new ITAG3.2 using SIFT4G software. This database with search function assists in inferring the influence of SNPs on the function of a target gene. This database can be used for selecting SNPs, which can be potentially deployed for improving tomato traits. Availability and implementation TGV is freely available at http://psd.uohyd.ac.in/tgv.