McCarthy, Charley G.P. and Fitzpatrick, David A. (2019) Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. Genes, 10 (521). ISSN 2073-4425

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Abstract

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.

Item Type:	Article
Additional Information:	© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Keywords:	pangenomes; bioinformatics; microbial eukaryotes; fungi;
Academic Unit:	Faculty of Science and Engineering > Research Institutes > Human Health Institute
Item ID:	11048
Identification Number:	https://doi.org/10.3390/genes10070521
Depositing User:	David Fitzpatrick
Date Deposited:	17 Sep 2019 13:44
Journal or Publication Title:	Genes
Publisher:	MDPI
Refereed:	Yes
URI:	https://www.mdpi.com
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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