scholarly journals Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 521 ◽  
Author(s):  
McCarthy ◽  
Fitzpatrick
Keyword(s):  
Genome Analysis ◽  
Oleaginous Yeast ◽  
Gene Prediction ◽  
Respiratory Pathogen ◽  
Computational Pipeline ◽  
Pan Genome ◽  
Genome Data ◽  
Microbial Eukaryotes ◽  
Functional Characterisation ◽  
Yeast Yarrowia Lipolytica

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.

scholarly journals Stable isotope and chemical inhibition analyses suggested the existence of a non-mevalonate-like pathway in the yeast Yarrowia lipolytica

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sivamoke Dissook ◽  
Tomohisa Kuzuyama ◽  
Yuri Nishimoto ◽  
Shigeru Kitani ◽  
Sastia Putri ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
Oleaginous Yeast ◽  
Isoprenoid Biosynthesis ◽  
Mep Pathway ◽  
Authentic Standard ◽  
Chemical Inhibition ◽  
Chromatographic Peaks ◽  
Methyl Erythritol Phosphate ◽  
Limiting Condition ◽  
Yeast Yarrowia Lipolytica

AbstractMethyl erythritol phosphate (MEP) is the metabolite found in the MEP pathway for isoprenoid biosynthesis, which is known to be utilized by plants, algae, and bacteria. In this study, an unprecedented observation was found in the oleaginous yeast Yarrowia lipolytica, in which one of the chromatographic peaks was annotated as MEP when cultivated in the nitrogen limiting condition. This finding raised an interesting hypothesis of whether Y. lipolytica utilizes the MEP pathway for isoprenoid biosynthesis or not, because there is no report of yeast harboring the MEP pathway. Three independent approaches were used to investigate the existence of the MEP pathway in Y. lipolytica; the spiking of the authentic standard, the MEP pathway inhibitor, and the 13C labeling incorporation analysis. The study suggested that the mevalonate and MEP pathways co-exist in Y. lipolytica and the nitrogen limiting condition triggers the utilization of the MEP pathway in Y. lipolytica.

Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica

2013 ◽  
Vol 98 (1) ◽  
pp. 251-262 ◽  
Author(s):  
A. Beopoulos ◽  
J. Verbeke ◽  
F. Bordes ◽  
M. Guicherd ◽  
M. Bressy ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Ricinoleic Acid ◽  
Yarrowia Lipolytica ◽  
Acid Production ◽  
Oleaginous Yeast ◽  
Yeast Yarrowia Lipolytica

Heterologous production of pentane in the oleaginous yeast Yarrowia lipolytica

2013 ◽  
Vol 165 (3-4) ◽  
pp. 184-194 ◽  
Author(s):  
John Blazeck ◽  
Leqian Liu ◽  
Rebecca Knight ◽  
Hal S. Alper
Keyword(s):  
Yarrowia Lipolytica ◽  
Oleaginous Yeast ◽  
Heterologous Production ◽  
Yeast Yarrowia Lipolytica

scholarly journals Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

2020 ◽  
Author(s):  
Idowu Olawoye ◽  
Simon D.W. Frost ◽  
Christian T. Happi
Keyword(s):  
West Africa ◽  
Genome Analysis ◽  
West African ◽  
Multiple Copy ◽  
Genome Sequences ◽  
Animal Reservoir ◽  
Pan Genome ◽  
Lineage Specificity ◽  
Mycobacterium Africanum ◽  
Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

scholarly journals Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems

2016 ◽  
Vol 8 (2) ◽  
pp. 387-402 ◽  
Author(s):  
Emilie Dumas ◽  
Eva Christina Boritsch ◽  
Mathias Vandenbogaert ◽  
Ricardo C. Rodríguez de la Vega ◽  
Jean-Michel Thiberge ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Secretion Systems ◽  
Pan Genome ◽  
Type Vii Secretion
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