Horticulture Research

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Article|17 Sep 2025|OPEN

TVIR 2.0: an enhanced database of the vegetables information resources

Tong Yu¹ ^,† , Xiao Ma¹ ^,† , Zhuo Liu¹ ^,† , Tongbing Su² , Chenhao Zhang¹ , Lusheng Guo¹ , Zipeng Meng¹ , Di Guo¹ , Nana Yao¹ , Yingchao Zhang¹ ^, , Haibin Liu¹ ^, and Xiaoming Song,^1,3 ^,

¹School of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China
²State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
³National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China
*Corresponding author. E-mail: zhangyc@ncst.edu.cn,liuhaibinhappy1013@126.com,songxm@ncst.edu.cn
^†Tong Yu,Xiao Ma and Zhuo Liu contributed equally to the study.

Horticulture Research 13,
Article number: uhaf239 (2026)
doi: https://doi.org/10.1093/hr/uhaf239
Views: 63

Received: 04 May 2025
Accepted: 03 Sep 2025
Published online: 17 Sep 2025

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.