TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. Issue 1 (19th September 2022)

• Record Type: Journal Article
• Authors: Yu, Tong; Ma, Xiao; Liu, Zhuo; Feng, Xuehuan; Wang, Zhiyuan; Ren, Jun; Cao, Rui; Zhang, Yingchao; Nie, Fulei; Song, Xiaoming
• Is Part Of: Horticulture research. Volume 9:Issue 1(2022)
• Publication Date: 2022-09-19
• Subjects: TVIR -- Vegetables -- Functional genes -- Gene annotation -- m6A -- CRISPR -- Tools; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1093/hr/uhac213
• Languages: English
• ISSNs: 2052-7276

Abstract

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 Resources' (TVIR, http://tvir.bio2db.com )—was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5, 215 auxin genes, 2, 437 anthocyanin genes, 15, 002 flowering genes, 79, 830 resistance genes, and 2, 639 glucosinolate genes of 59 vegetables. In addition, 2, 597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1, 058 erasers, and 1, 026 readers. A total of 2, 101, 501 specific clustered regularly interspaced short palindromic repeats (CRISPR) guide sequences and 17, 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs was also provided for 59 vegetable species. TVIR database contains 2, 346, 850 gene annotations by Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools were 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 were 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.