Genome Evolution Laboratory, Department of Biology, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
Human Health Research Institute, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
Genes (Basel). 2019 Jul 10;10(7):521. doi: 10.3390/genes10070521.
Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss's capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen . Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub.
尽管泛基因组概念起源于原核生物基因组学，但也有越来越多的真核生物物种泛基因组被分析。然而，与原核生物相比，用于真核生物泛基因组分析的软件相对较少。在之前的研究中，我们使用一种计算流程分析了四种模式真菌的泛基因组，该流程使用基于共线性的泛基因组同源聚类工具（PanOCT）方法构建泛基因组。在这里，我们提出了该流程的一个修改和改进版本，我们称之为 Pangloss。Pangloss 可以为用户提供的一组给定物种的基因组进行基因预测，使用 PanOCT 从该组中构建和（可选）精炼物种泛基因组，并可以对物种泛基因组数据进行各种功能特征和可视化分析。为了展示 Pangloss 的功能，我们构建并分析了油脂酵母的物种泛基因组，还重建了先前发表的机会性呼吸道病原体的物种泛基因组。Pangloss 是用 Python、Perl 和 R 实现的，并通过 GitHub 以开源 GPLv3 许可证免费提供。
