Yu Tong, Ma Xiao, Liu Zhuo, Feng Xuehuan, Wang Zhiyuan, Ren Jun, Cao Rui, Zhang Yingchao, Nie Fulei, Song Xiaoming
School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China.
Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Hortic Res. 2022 Sep 19;9:uhac213. doi: 10.1093/hr/uhac213. eCollection 2022.
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.
蔬菜是人类日常饮食中不可或缺的一部分。因此，系统地研究蔬菜的基因组数据并构建一个数据共享与分析平台至关重要。在本研究中，基于59种蔬菜的基因组构建了一个具有用户友好型网络界面的综合性蔬菜平台——蔬菜信息资源库（TVIR，http://tvir.bio2db.com）。TVIR数据库包含众多重要的功能基因，包括59种蔬菜的5215个生长素基因、2437个花青素基因、15002个开花基因、79830个抗性基因和2639个芥子油苷基因。此外，还鉴定出2597个N6-甲基腺苷（m6A）基因，包括513个写入器、1058个擦除器和1026个读取器。共检测到2101501条特异性成簇规律间隔短回文重复序列（CRISPR）引导序列和17377个微小RNA（miRNA），并将其存入TVIR数据库。还提供了59种蔬菜的基因共线性、重复和直系同源信息。TVIR数据库通过瑞士蛋白质数据库（Swiss-Prot）、跨膜蛋白数据库（TrEMBL）、基因本体论（GO）、蛋白质家族数据库（Pfam）和非冗余数据库（Nr）进行了2346850条基因注释。提供了共线性、引物设计、Blast和JBrowse工具，以方便用户进行比较基因组分析。这是首次大规模收集蔬菜基因组数据并进行生物信息学分析。所有基因组和基因序列、注释及生物信息学结果均可从TVIR轻松下载。此外，已收集整理了98种蔬菜的转录组数据，可按物种、组织或不同生长阶段进行搜索。TVIR有望成为全球蔬菜研究的关键枢纽。该数据库未来将随着新组装的蔬菜基因组和比较基因组研究不断更新。
