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PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph
[article]
2019
bioRxiv
pre-print
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The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative ...
We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. ...
Acknowledgements We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo. ...
doi:10.1101/836239
fatcat:utqwlatqkncbleusf2edbx54ei
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
2020
PLoS Computational Biology
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
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The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative ...
We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. ...
Acknowledgments We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo. ...
doi:10.1371/journal.pcbi.1007732
pmid:32191703
pmcid:PMC7108747
fatcat:ff6ccvwavzcutaxtxcvntfb74e
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
2019
Nucleic Acids Research
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We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. ...
Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial ...
each PPanGGOLiN partition. ...
doi:10.1093/nar/gkz926
pmid:31647104
pmcid:PMC7145621
fatcat:dwdxeaytnvar7iq3kudicrcz2q
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome
[article]
2021
bioRxiv
pre-print
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A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense ...
To gain insight into D. pigrum's chromosomal structure, pangenome and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. ...
(B) This PPanGGOLiN partitioned pangenome graph displays the overall genomic diversity of the 28 D. pigrum genomes. ...
doi:10.1101/2021.04.16.440249
fatcat:rhfoq3rwv5d6daaeohmn4whnau
Evidence for selection in a prokaryote pangenome
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
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A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. ...
Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable. ...
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. Blanchet, F. G., Cazelles, K. & Gravel, D. Co-occurrence is not evidence of ecological interactions. ...
doi:10.1101/2020.10.28.359307
fatcat:whzhx6jbefdzbgadrseybhaxki
Construction of a complete set of Neisseria meningitidis defined mutants - the NeMeSys collection - and its use for the phenotypic profiling of the genome of an important human pathogen
[article]
2020
bioRxiv
pre-print
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The NeMeSys collection is an invaluable resource paving the way for a global phenotypic landscape in a major human bacterial pathogen. ...
Even in model bacterial species, there is a sizeable proportion of such genes, which has important theoretical and practical consequences. ...
PPanGGOLiN: Depicting microbial diversity via a partitioned 741 pangenome graph. PLoS Comput. Biol. 16, e1007732 (2020). 742 22. Hutchison, C.A. et al. ...
doi:10.1101/2020.08.12.247981
fatcat:oapiryjhkngmhakm7jpoj442rq
Plateforme numérique pour l'antibiorésistance, ABRomics
[article]
2021
Zenodo
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Antibiotic resistance (ABR) is a major public health problem and a threat for the future. ...
It covers the diversity of ABR research in clinical and fundamental fields, mathematical modeling methods and the whole range of expertise in computer science, bioinformatics, database and computer architecture ...
The development of the Meta-PanGenomic graph method will be conducted in strong interaction with WP3 of ABROmics, particularly in Task 3.3.1. ...
doi:10.5281/zenodo.5230261
fatcat:lhtpmfwdjnddhi6cdilfpccc7q
Evidence for selection in the abundant accessory gene content of a prokaryote pangenome
2021
Molecular biology and evolution
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Keyword: pangenome, microbial genomics, selection. ...
A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. ...
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. 520 PLoS Computational Biology . 521 [Goyal2018] Goyal, A. 2018. ...
doi:10.1093/molbev/msab139
pmid:33963386
pmcid:PMC8382901
fatcat:hear75o4wjafralefr47ohe3za