The genomic database of fruits: A comprehensive fruit information database for comparative and functional genomic studies
Jingyi Liu, Chenchen Huang, Dingsheng Xing, Shujing Cui, Yanhong Huang, Can Wang, Ruohan Qi, Zhuo Liu, Rong Zhou, Xiao Ma, Xiaoming Song
Abstract
Fruit has an important role in human nutrition and health; therefore, the systematic study of fruit genomic data is essential. The Genomic Database of Fruits (TGDF, http://tgdf.bio2db.com/), established through whole-genome analyses of 44 fruit species, is a comprehensive, user-friendly fruit database. TGDF contains a wealth of functional genes, including 11,350 flowering genes, 3,161 auxin signaling genes, 2,164 anthocyanin synthesis genes, 1,464 abscisic acid (ABA) synthesis genes, 10,931 cell division and expansion genes, 1,786 starch synthesis genes, 294 fruit size genes, and 6,311 sugar transporter genes. Additionally, TGDF contains 1,433,368 CRISPR guide sequences from various fruit genomes, along with information on homologous genes and duplication types for the 44 fruit species. TGDF contains 6,417,060 gene annotations sourced from TrEMBL, SwissProt, Nr, and Gene Ontology databases, along with tools such as Sequence Fetch, BLAST, Synteny, and JBrowse for bioinformatics analyses. Transcriptomic data were also collected and collated from fruits, including details on instruments, tissues, or growth stages. This comprehensive, user-friendly resource is the first collection of fruit genomic data. Users can easily download genomic sequences, gene annotations, and bioinformatics analysis results from TGDF, which will be updated continually. We anticipate that TGDF will become a primary resource for fruit comparative and functional genomic studies.