The Onion Genomic Resource: A genomics and bioinformatics driven resource for onion breeding

Abstract

Onion (Allium cepa L.), often regarded as a crop having an antediluvian coexistence with humans, is by far one of the most challenging plant species to be worked on, especially with respect to delineating its genomic information. It is considered as a plant of immense culinary and medicinal importance. However, there are very limited genomic ventures that have so far been established that could shed light on some of the most captivating aspects of the onion genome. Onion Genomic Resource (OGR), with three-tier architecture, is the first of its kind, comprehensive web-resource/database, built in MySQL database and PHP that catalogues the genomic developments specific to onion. It houses information of assembly of 20,204 publicly available onion expressed sequence tags (ESTs), available 20,755 assembled transcripts and 249,987 unigenes from Allium cepa transcriptome shotgun assembly (TSA) along with their annotations and functional significance. A total of 1915 SSRs from Onion ESTs and123,282 SSRs from Onion TSA data have been catalogued in OGR. Also, 135,424 SNPs and 11,891 Indels identified from Onion TSA data as well as 15 and 13 SNPs and Indels identified, respectively from Onion ESTs have been put in database. The resource also contains information of gene annotations, linked with KEGG pathways and 7 previously reported and 1 predicted onion miRNAs with their associated targets, which range from cytoplasmic globular proteins to membrane ion channels. Additionally, gene prediction was carried out for the unannotated sequences, of which few were observed to harbor coding regions for novel protein coding genes and transcripts that so far have not yet been identified. Over 200 different ready-to-use experimentally validated molecular markers were also mined from the existing literature to further enrich the lab-based studies targeting variety improvement. The OGR can be useful for onion molecular breeders as well as a valuable tool for confirmation of predicted ORF once the whole genome of onion is sequenced. The OGR is an open resource freely accessible at http://webtom.cabgrid.res.in/ogr/