TVIR 2.0: an enhanced database of the vegetables information resources

Hortic Res. 2025 Sep 17;12(12):uhaf239. doi: 10.1093/hr/uhaf239. eCollection 2025 Dec.

ABSTRACT

Since its inaugural release in 2022, The Vegetables Information Resources (TVIR) has been a cornerstone for genomics and genetic breeding studies within the vegetable research community. With advancements in sequencing technologies leading to an influx of new genome sequences, TVIR has been upgraded to version 2.0 (http://tvir2.bio2db.com/), expanding from 59 to 84 vegetable species and introducing new functional modules to accelerate research. This upgrade incorporates a CRISPR/Cas9 resource module, which integrates four specialized tools: CasFinder, CasOT, Crisflash, and CRISPRCasFinder, to facilitate gene editing research. The database further features dynamic synteny analysis with an interactive interface, enabling users to visualize genomic relationships between species. Additionally, two novel bioinformatics tools Hmmsearch and CRISPRCasViewer are integrated to enhance comparative and functional genomic analyses. TVIR 2.0 retains all TVIR 1.0 features while updating resistance gene identification, expanding from 3 to 8 types, and transcription factor datasets, now including 237 431 TFs, an increase from 172 493.The database integrates comprehensive genomic, transcriptomic, and functional annotation data, providing freely accessible resources for vegetable breeding and gene editing.

PMID:41378136 | PMC:PMC12685723 | DOI:10.1093/hr/uhaf239