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Article|19 Sep 2022|OPEN
TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies
Tong Yu1 ,† , Xiao Ma1 ,† , Zhuo Liu1 ,† , Xuehuan Feng2 ,† , Zhiyuan Wang1 , Jun Ren3 , Rui Cao1 , Yingchao Zhang1 , Fulei Nie1 and Xiaoming Song,1,2,4 ,
1School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
2Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
3Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
4School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
*Corresponding author. E-mail: songxm@ncst.edu.cn
†Tong Yu,Xiao Ma,Zhuo Liu and Xuehuan Feng contributed equally to the study.

Horticulture Research 9,
Article number: uhac213 (2022)
doi: https://doi.org/10.1093/hr/uhac213
Views: 221

Received: 08 Jun 2022
Accepted: 14 Sep 2022
Published online: 19 Sep 2022

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.