Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

Tonkin‐Hill, Gerry; MacAlasdair, Neil; Ruis, Christopher; Weimann, Aaron; Horesh, Gal; Lees, John A.; Gladstone, Rebecca A.; Lo, Stephanie; Beaudoin, Christopher; Floto, R. Andres; Frost, Simon D. W.; Corander, Jukka; Bentley, Stephen D.; Parkhill, Julian

doi:10.1101/2020.01.28.922989

Cited by 118 publications

(147 citation statements)

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“…Plasmids were annotated using Prokka (version 1.14.6) [39]. Pangenome analysis used Panaroo (version 1.2.2) [40]. Core genes, soft core genes, shell genes and cloud genes are those found in [100, 99], (99, 95], (95, 15], and (15, 0] percent of sequences respectively.…”

Section: Discussionmentioning

confidence: 99%

Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock

Chau

AbuOun

et al. 2020

Preprint

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IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

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Section: Discussionmentioning

confidence: 99%

Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock

Chau

AbuOun

et al. 2020

Preprint

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“…Additionally, the pan-genome functional analysis was carried out 120 utilizing KEGG, COG metabolic and functional pathways, which were all visualised with LibreOffice Calc plot functions. Panaroo (26) and PopPUNK (27) were also employed for pangenome investigation of gene profiles and clustering core and accessory genomes.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Pan-genome analysis ofMycobacterium africanum: insights to dynamics and evolution

Olawoye

2020

Preprint

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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 30 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 (MAF) might have emigrated out of West Africa but was outcompeted by more virulent strains of M. tuberculosis (MTB).35 Whole genome sequences of MTB from Nigeria (n=21), China (n=21) and MAF from Mali (n=24) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. The outcome of this analysis shows that Lineages 4, 5 and 6 have relatively close pan-genomes whilst lineage 2 has an open 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 40 geographical distribution of these lineages.The findings in this study provides a perspective to one of the hypotheses that M. africanum might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.3 Introduction:

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“…We did this using a custom mapping, variant calling, and local realignment around indels pipeline using bwa-MEM (Li, 2013), samtools mpileup (Li, 2011), and MUSCLE (Edgar, 2004), and then used the resulting whole-genome pseudo alignments to infer phylogenies for each cluster, using gubbins (Croucher et al, 2014), and RAxML, its underlying dependency (Stamatakis, 2014). In order to construct a phylogeny for the entire collection, and also the collection combined with global isolates, we used the newly published panaroo pan-genome pipeline (Tonkin-Hill et al, 2020) to infer a set of core genes for the entire collection. We concatenated alignments of all the core genes, and then used IQ-TREE (Nguyen et al, 2014), with the substitution model, GTR+F+I+G4, inferred by ModelFinder (Kalyaanamoorthy et al, 2017), to infer phylogenies for both the entire Burkina Faso collection and the Burkina Faso collection plus global isolates.…”

Section: R a F Tmentioning

confidence: 99%

The effect of recombination on the evolution of a population ofNeisseria meningitidis

MacAlasdair

Pesonen

Brynildsrud

et al. 2020

Preprint

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Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of indepth investigation of the genomic events associated with routine pathogen transmission. Here we fill this knowledge gap by a detailed analysis of 2,839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009-2012. Our findings indicate that the meningococcal genome is highly dynamic, with recombination hotspots and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate the profound effect of population structure on genome flexibility, with some lineages in Burkina Faso being orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programmes and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern. meningicoccus | recombination | bacteria | evolution Correspondence: nm12@sanger.ac.uk

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Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

Cited by 118 publications

References 50 publications

Genomic network analysis of an environmental and livestock IncF plasmid population

Genomic network analysis of an environmental and livestock IncF plasmid population

Pan-genome analysis ofMycobacterium africanum: insights to dynamics and evolution

The effect of recombination on the evolution of a population ofNeisseria meningitidis

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