LettuceGDB: The community database for lettuce genetics and omics

文献类型： 外文期刊

第一作者： Guo, Zhonglong

作者： Guo, Zhonglong;Li, Bo;Du, Jianjun;Shen, Fei;Zhao, Yongxin;Deng, Yang;Kuang, Zheng;Lu, Xianju;Wang, Ying;Wei, Jianhua;Guo, Xinyu;Zhao, Chunjiang;Yang, Xiaozeng;Guo, Zhonglong;Tao, Yihan;Wan, Miaomiao;Wang, Ying;Li, Lei;Guo, Zhonglong;Tao, Yihan;Wan, Miaomiao;Wang, Ying;Li, Lei;Guo, Zhonglong;Li, Bo;Shen, Fei;Zhao, Yongxin;Deng, Yang;Kuang, Zheng;Wang, Ying;Yang, Xiaozeng;Guo, Zhonglong;Du, Jianjun;Lu, Xianju;Guo, Xinyu;Zhao, Chunjiang;Wang, Dong;Han, Yingyan

作者机构：

关键词： lettuce; genome; multi-omics; germplasms; breeding; community

期刊名称：PLANT COMMUNICATIONS （ 影响因子：10.5； 五年影响因子：10.5 ）

ISSN： 2590-3462

年卷期： 2023 年 4 卷 1 期

页码：

收录情况： SCI

摘要： 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.

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