Abstract

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

中文翻译：

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GreenPhylDB v5：植物基因组比较泛基因组数据库

摘要

比较基因组学是对不同物种之间基因组关系的分析，是进化和功能基因组研究的重要基础。GreenPhylDB (https://www.greenphyl.org) 是一个数据库，旨在促进植物基因组之间的基因家族和同源关系的探索，包括对全球粮食安全至关重要的主要作物。GreenPhylDB 自 2007 年拟南芥和水稻基因组发布后推出，并经历了多次发布。鉴于目前可用的植物基因组数量，为比较基因组学研究选择单一参考变得具有挑战性，但仍然缺乏利用按物种划分的多个基因组进行直系同源检测的数据库。GreenPhylDBv5 通过利用按物种划分的多个基因组序列引入了比较泛基因组学的概念。我们创造了 19 个泛基因，并将它们与仍然依赖同一个基因组的其他物种一起加工。总共考虑了 46 种植物物种来构建基因家族并通过基于系统发育的分析预测它们的同源关系。此外，自上次发布以来，我们对网站进行了更新，并添加了一套新的原创工具，包括蛋白质域组合、树拓扑搜索以及供用户存储自己的结果的部分，以支持社区管理工作。