Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes
Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes
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DOI：
10.3390/genes10070521
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发表时间：
2019-07-01
期刊：
影响因子：
3.5
通讯作者：
Fitzpatrick, David A.
中科院分区：
文献类型：
--
作者：
McCarthy, Charley G. P.;Fitzpatrick, David A.
虽然泛基因组概念起源于原核生物基因组学，但越来越多的真核生物物种泛基因组也被分析。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缺乏。在以前的研究中，我们分析了四种模式真菌的泛基因组与计算管道，构建泛基因组使用同线性依赖泛基因组同源聚类工具（PanOCT）的方法。在这里，我们提出了一个修改和改进版本的管道，我们称之为Pangloss。Pangloss可以对用户提供的给定物种的一组基因组进行基因预测，使用PanOCT构建并可选地从该组中提炼物种泛基因组，并且可以对物种泛基因组数据进行各种功能表征和可视化分析。为了证明Pangloss的能力，我们构建并分析了产油酵母解脂耶氏酵母的物种泛基因组，并重建了先前发表的机会性呼吸道病原体烟曲霉的物种泛基因组。Pangloss是用Python、Perl和R实现的，并通过GitHub在开源GPLv3许可下免费提供。
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 Yarrowia lipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub.