Wheatgene: a genomics database for common wheat and its related species

Diego F. Garcia, Zhengyu Wang, Jiantao Guan, Lingjie Yin, Shuaifeng Geng, Aili Li, Long Mao
2021 Crop Journal  
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.
more » ... e, 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. WheatGene is available at http://wheatgene.agrinome.org. Long Mao conceptualized the database and supervised the entire development process. Diego Fernando Garcia executed and developed the database. Jiantao Guan, Zenyu Wang, Shuaifeng Geng, and Aili Li provided biological consultation. Lingjie Yin provided the computational environment and set up the distribution of the database. Diego Fernando Garcia wrote the first draft and together with Long Mao finalized the manuscript.
doi:10.1016/j.cj.2021.04.011 fatcat:vldc7glrmbdtviscpafkdcgx2e