TVIR 2.0: an enhanced database of the vegetables information resources

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.

Acknowledgments

This work was supported by the National Key Research and Development Program of China (2023YFF1002000), the Tangshan Science and Technology Plan Project (24130219C), the Basic Research Program of Tangshan (22130231H), the Basic research expenses for provincial universities (JJC2024001), the National Natural Science Foundation of China (32172583), Basic Research Funds for Provincial Universities Basic Research Projects of North China University of Science and Technology (JQN2023036), Youth Scholars Promotion Plan of North China University of Science and Technology (QNTJ202308), the S&T Program of Hebei (23372505D), and the Hebei Natural Science Foundation (H2023209084).

Author contributions

X.S. conceived the project and was responsible for the initiation of the project. X.S., X.M., Y.Z., H.L., and T.Y. supervised and managed the project and research. Data generation and collection were performed by X.S., T.Y., X.M., T.S., C.Z., N.Y., and Z.M. Bioinformatics analysis and database construction was led by X.S., T.Y., Z.L., and L.G. The manuscript was organized, written, and revised by X.S., T.Y., X.M., Z.L., T.S., D.G., Y.Z., and H.L. All the authors read and revised the manuscript.

Data availability

TVIR 2.0 is freely available to the public without any registration or login requirements (http://tvir2.bio2db.com/). All the related datasets can be downloaded from the database.

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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