Large-scale comparative analysis of microbial pan-genomes using PanOCT

Inman, Jason M.; Beck, Erin; Brinkac, Lauren; Clarke, Thomas H.; Fouts, Derrick E.

doi:10.1093/bioinformatics/bty744

Cited by 17 publications

(16 citation statements)

References 6 publications

(6 reference statements)

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“…Roary outputs can be visualized with Phandango ( Hadfield et al, 2017 ) and R scripts were used to view the resulting outputs. Pangenomes were also analyzed using PanOCT ( Fouts et al, 2012 ) in conjunction with the JCVI pipeline and PanACEA visualization tool ( Inman et al, 2019 ). PanOCT and Roary are both especially useful for clustering genes from closely related species/strains.…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

et al. 2020

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Section: Methodsmentioning

confidence: 99%

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

et al. 2020

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“…Recently, core- and pan-genomes have been used for the comparative analysis of multiple genomes, with multiple tools being developed [13,20,21,22]. Their biggest advantage is taking into account all functional genes existing in the pan-genome of the study.…”

Section: Resultsmentioning

confidence: 99%

Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections

et al. 2019

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The surveillance of health care-associated infection (HAI) is an essential element of the infection control program. While whole-genome sequencing (WGS) has widely been adopted for genomic surveillance, its data processing remains to be improved. Here, we propose a three-level data processing pipeline for the precision genomic surveillance of microorganisms without prior knowledge: species identification, multi-locus sequence typing (MLST), and sub-MLST clustering. The former two are closely connected to what have widely been used in current clinical microbiology laboratories, whereas the latter one provides significantly improved resolution and accuracy in genomic surveillance. Comparing to a broadly used reference-dependent alignment/mapping method and an annotation-dependent pan-/core-genome analysis, we implemented our reference- and annotation-independent, k-mer-based, simplified workflow to a collection of Acinetobacter and Enterococcus clinical isolates for tests. By taking both single nucleotide variants and genomic structural changes into account, the optimized k-mer-based pipeline demonstrated a global view of bacterial population structure in a rapid manner and discriminated the relatedness between bacterial isolates in more detail and precision. The newly developed WGS data processing pipeline would facilitate WGS application to the precision genomic surveillance of HAI. In addition, the results from such a WGS-based analysis would be useful for the precision laboratory diagnosis of infectious microorganisms.

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“…subtilis and E. coli initial pan-genomes were based on the RefSeq annotation of these genomes. The pan-genome was generated using the pan-genome pipeline at the J. Craig Venter Institute (JCVI) at the nucleotide level using default parameters (25). This (which was not certified by peer review) is the author/funder.…”

Section: Methodsmentioning

confidence: 99%

A pan-genome method to determine core regions of theBacillus subtilisandEscherichia coligenomes

Fogel

Abramson

Brinkac

et al. 2020

Preprint

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Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. We show that these core regions are very likely to contain all or almost all essential genes. We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species. ImportanceThe pan-genome approach presented in this paper can be used to determine core regions of a genome and has many possible applications. Synthetic engineering design can be informed by which genes/regions are more conserved (core) versus less conserved. The level of conservation of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or system that can inform researchers about possible functional significance. The pattern of gene presence across the different genomes of a species can inform the understanding of evolution and horizontal gene acquisition. The approach saves considerable time and effort relative to laboratory methods used to identify essential genes in species.insertion of clusters 8068, 8300, 8069, and 8070 where both 8068 and 8070 are annotated as ftsZ.Gene rodA (cluster 3994 in 97 genomes) is replaced by either: cluster 8718 (2 genomes) or clusters 10492, 6436, and 6437 (1 genome) or clusters 6436 and 6437 (8 genomes) where 8718 and 6436 are annotated as rodA. For B. subtilis spp. spizizenii strain W23, poly(ribitol phosphate) is the main teichoic acid (16) and this was thought to distinguish spp. spizizenii from spp. subtilis whose type strain 168 has poly(glycerol phosphate) as the main teichoic acid. Further study found that the ribitol/glycerol distinction does not distinguish between spizizenii and subtilis subspecies (17) but rather either subspecies can contain one or the other. Our PGG confirms this and in fact finds six distinct vairieties of the WTA region. For example the tagD gene (cluster 4748 in 35 genomes) has been replaced by mutlitple orthologs with the same annotation: cluster 3746 (23 genomes), cluster 5431 (43 genomes), cluster 6915 (2 g...

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Large-scale comparative analysis of microbial pan-genomes using PanOCT

Abstract: Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.

Cited by 17 publications

References 6 publications

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections

A pan-genome method to determine core regions of theBacillus subtilisandEscherichia coligenomes

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