GreenPhylDB: A phylogenomic database for plant comparative genomics

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.

GreenPhylDB（网址：https://www.greenphyl.org）是一款旨在推动植物基因组间基因家族与同源关系探索的专业数据库，其涵盖了对全球粮食安全具有关键意义的主粮作物。该数据库自2007年正式上线，彼时拟南芥（Arabidopsis thaliana）与水稻（Oryza sativa）的基因组刚刚完成发布，且此后历经多次版本迭代。随着当前可用植物基因组数量的持续增长，为比较基因组学研究遴选单一参考基因组已颇具挑战，但目前仍缺乏能够利用单物种多套基因组开展直系同源基因检测（orthology detection）的数据库。GreenPhylDBv5引入了比较泛基因组学（comparative pangenomics）的研究理念，通过整合单物种的多套基因组序列开展相关研究。我们共构建了19个泛基因（pangenes），并将其与其他仍仅依赖单份参考基因组的物种完成了联合分析处理。本次研究总计纳入46种植物，用于构建基因家族并通过基于系统发育的分析方法预测其同源关系。

搜集汇总

背景与挑战

背景概述

GreenPhylDB是一个专注于植物比较与功能基因组学的数据库。其版本5.1整合了19个泛基因组和27个参考基因组，涵盖46个物种，并通过系统发育分析方法预测基因家族的同源关系。