McCarthy, Charley G.P. and Fitzpatrick, David A. (2019) Pan-genome analyses of model fungal species. Microbial Genomics, 5 (2). 000243. ISSN 2057-5858

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Abstract

The concept of the species ‘pan-genome’, the union of ‘core’ conserved genes and all ‘accessory’ non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining ‘accessory’ gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.

Item Type:	Article
Additional Information:	ã 2019 The Authors This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords:	fungal pangenomes; comparative genomics; yeast; Aspergillus; Cryptococcus;
Academic Unit:	Faculty of Science and Engineering > Research Institutes > Human Health Institute
Item ID:	11051
Identification Number:	https://doi.org/10.1099/mgen.0.000243
Depositing User:	David Fitzpatrick
Date Deposited:	17 Sep 2019 15:20
Journal or Publication Title:	Microbial Genomics
Publisher:	Microbiology Society
Refereed:	Yes
URI:	https://www.microbiologyresearch.org/
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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