WheatGene: A genomics database for common wheat and its related species

文献类型： 外文期刊

第一作者： Garcia, Diego F.

作者： Garcia, Diego F.;Wang, Zhengyu;Guan, Jiantao;Yin, Lingjie;Geng, Shuaifeng;Li, Aili;Mao, Long

作者机构：

关键词： Wheat; Genome; Comparative genomics; Database; Genome browser

期刊名称：CROP JOURNAL （ 影响因子：4.647； 五年影响因子：5.781 ）

ISSN： 2095-5421

年卷期： 2021 年 9 卷 6 期

页码：

收录情况： SCI

摘要： Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) derived from genetically related tetraploid wheat T. turgidum (AABB) and a diploid goatgrass Aegilops tauschii (DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here, we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST, synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. (C) 2021 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.

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