TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies

Authors

Tong Yu, North China University of Science and Technology
Xiao Ma, North China University of Science and Technology
Zhuo Liu, North China University of Science and Technology
Xuehuan Feng, University of Nebraska-LincolnFollow
Zhiyuan Wang, North China University of Science and Technology
Jun Ren, Chinese Academy of Agricultural Sciences
Rui Cao, North China University of Science and Technology
Yingchao Zhang, North China University of Science and Technology
Fulei Nie, North China University of Science and Technology
Xiaoming Song, North China University of Science and Technology, University of Nebraska-Lincoln, University of Electronic Science and Technology of China

Document Type

Article

Date of this Version

12-1-2022

Citation

Horticulture Research, 2022, 9: uhac213 https://doi.org/10.1093/hr/uhac213

Comments

Open access.

Abstract

Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface—The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)—was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.