Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes.
bioinformatics
fungi
microbial eukaryotes
pangenomes
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
10 07 2019
10 07 2019
Historique:
received:
07
06
2019
revised:
05
07
2019
accepted:
05
07
2019
entrez:
13
7
2019
pubmed:
13
7
2019
medline:
13
7
2019
Statut:
epublish
Résumé
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
Identifiants
pubmed: 31295964
pii: genes10070521
doi: 10.3390/genes10070521
pmc: PMC6678930
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
Supplementary Materials: The following are available online at www.mdpi.com/xxx/s1. Table S1, Information for Yarrowia lipolytica and Aspergillus fumigatus pan-genome datasets. Core gene models labelled in green, accessory gene models labelled in red. References and strain information taken from cited articles where available, otherwise from GenBank or similar resources with relevant links included. Table S2. GO-slim enrichment analysis for the Yarrowia lipolytica pan-genome dataset. Fischer’s exact test with FDR correction (p < 0.05) carried out using GOATools within Pangloss. All terms present in the table are either significantly over- or under-represented in either the Y. lipolytica core or accessory genome. Significantly over-represented terms labelled green, significantly under-represented terms labelled red.
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