LettuceGDB: The community database for lettuce genetics and omics

• Published in: Plant communications Vol. 4; no. 1; p. 100425
• Main Authors: Guo, Zhonglong, Li, Bo, Du, Jianjun, Shen, Fei, Zhao, Yongxin, Deng, Yang, Kuang, Zheng, Tao, Yihan, Wan, Miaomiao, Lu, Xianju, Wang, Dong, Wang, Ying, Han, Yingyan, Wei, Jianhua, Li, Lei, Guo, Xinyu, Zhao, Chunjiang, Yang, Xiaozeng
• Format: Journal Article
• Language: English
• Published: China Elsevier Inc 09-01-2023; Elsevier
• Subjects: breeding; community; genome; Genomics; Genotype; germplasms; Lactuca - genetics; lettuce; multi-omics; Phenotype; Plants; Resource; multi-omics; genome; community; germplasms; lettuce; breeding
• ISSN: 2590-3462; 2590-3462
• DOI: 10.1016/j.xplc.2022.100425

As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.
LettuceGDB, which contains multi-omics data and integrates rich germplasm resources with abundant phenotypic data, is a comprehensive lettuce database dedicated to data mining and database-driven exploration for scientific research and lettuce breeding. As a community database, LettuceGDB aims to provide information and promote knowledge sharing to serve the lettuce research community.