Wang Yi
USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, USA.
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
Plant Cell Physiol. 2017 Jan 1;58(1):e2. doi: 10.1093/pcp/pcw210.
RNA-based gene duplication, known as retrocopy, plays important roles in gene origination and genome evolution. The genomes of many plants have been sequenced, offering an opportunity to annotate and mine the retrocopies in plant genomes. However, comprehensive and unified annotation of retrocopies in these plants is still lacking. In this study I constructed the PlantRGDB (Plant Retrocopied Gene DataBase), the first database of plant retrocopies, to provide a putatively complete centralized list of retrocopies in plant genomes. The database is freely accessible at http://probes.pw.usda.gov/plantrgdb or http://aegilops.wheat.ucdavis.edu/plantrgdb. It currently integrates 49 plant species and 38,997 retrocopies along with characterization information. PlantRGDB provides a user-friendly web interface for searching, browsing and downloading the retrocopies in the database. PlantRGDB also offers graphical viewer-integrated sequence information for displaying the structure of each retrocopy. The attributes of the retrocopies of each species are reported using a browse function. In addition, useful tools, such as an advanced search and BLAST, are available to search the database more conveniently. In conclusion, the database will provide a web platform for obtaining valuable insight into the generation of retrocopies and will supplement research on gene duplication and genome evolution in plants.
基于RNA的基因复制，即反转录拷贝，在基因起源和基因组进化中发挥着重要作用。许多植物的基因组已被测序，这为注释和挖掘植物基因组中的反转录拷贝提供了契机。然而，这些植物中反转录拷贝的全面统一注释仍然缺乏。在本研究中，我构建了PlantRGDB（植物反转录基因数据库），这是首个植物反转录拷贝数据库，旨在提供植物基因组中假定完整的反转录拷贝集中列表。该数据库可通过http://probes.pw.usda.gov/plantrgdb或http://aegilops.wheat.ucdavis.edu/plantrgdb免费访问。它目前整合了49种植物和38997个反转录拷贝以及特征信息。PlantRGDB提供了一个用户友好的网络界面，用于搜索、浏览和下载数据库中的反转录拷贝。PlantRGDB还提供了集成图形查看器的序列信息，用于显示每个反转录拷贝的结构。使用浏览功能报告每个物种反转录拷贝的属性。此外，还有一些有用的工具，如高级搜索和BLAST，可更方便地搜索数据库。总之，该数据库将提供一个网络平台，以深入了解反转录拷贝的产生，并将补充植物基因复制和基因组进化的研究。
