Roary: rapid large-scale prokaryote pan genome analysis

Page, Andrew J.; Cummins, Carla; Hunt, Martin; Wong, Vanessa; Reuter, Sandra; Holden, Matthew T. G.; Fookes, María; Falush, Daniel; Keane, Jacqueline A.; Parkhill, Julian

doi:10.1093/bioinformatics/btv421

Cited by 3,813 publications

(3,114 citation statements)

References 9 publications

(12 reference statements)

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“…We generated alignments by mapping reads to the TIGR4 reference using bwa-mem v0.7.10 with default settings 21 , and called variants from these alignments using samtools v1.2 mpileup and bcftools call 22 . We used Roary 1.007001 23 with a 95% BLAST ID cutoff to construct a pan-genome from the annotated assemblies, from which a core gene alignment was extracted. We then created alignments by two further methods.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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“…Patterns of gene loss or gain across strains can be inferred from these inventories. Toward this end, we annotated each genome assembly using Prokka (Seemann 2014) and used Roary (Page et al 2015) to cluster orthologous coding sequences and generate a gene possession matrix (assemblies with more than 500 contigs were excluded). This identified 2148 orthologous clusters present in >99% of 209 strains (core genes), along with an additional 36,627 present in only a subset of strains (Table 4; Supplemental Text S3; Supplemental Fig.…”

Section: Pan-genome Analyses Identified Clade-specific Gene Content Imentioning

confidence: 99%

“…By using the Roary gene presence matrix (homologous clusters) (Page et al 2015), we found 8409 genes lost from at least one longitudinal series (Fig. 6C).…”

Section: Recurrent Genomic Changes In B Cenocepacia During Long-termmentioning

confidence: 99%

“…Pan-genome analyses for all isolates with fewer than 500 contigs or for each RAPD genotype were performed using the rapid large-scale prokaryote pan-genome analysis pipeline, Roary, v3.4.2, from the Sanger Institute (https://github.com/ sanger-pathogens/Roary; Page et al 2015).…”

Section: Pan-genome Analysesmentioning

confidence: 99%

“…To identify variants that are associated with a phenotypic variation, we first identified 3055 gene families that were present in at least four RAPD genotypes as defined by Prokka (Seemann 2014) and Roary (Page et al 2015). We excluded RAPD15 from the analyses due to small sample size (two isolates total).…”

Section: Identification Of Candidate Genotype-phenotype Associationsmentioning

confidence: 99%

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Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

et al. 2017

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Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2-20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.

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Surveillance for Colonization, Transmission, and Infection With Methicillin-Susceptible Staphylococcus aureus in a Neonatal Intensive Care Unit

et al. 2021

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Key Points Question What are the risk factors for the acquisition of methicillin-susceptible Staphylococcus aureus (MSSA) colonization and infections in a neonatal intensive care unit? Findings In this cohort study of 590 newborns, the acquisition of S aureus colonization and infection was monitored until hospital discharge. Colonization with MSSA was associated with lower birth weight, longer hospitalization, and higher odds of acquiring S aureus infection during hospitalization. Meaning These findings suggest that nasal colonization is a relevant risk factor for MSSA infection in a nonoutbreak neonatal intensive care unit setting.

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Roary: rapid large-scale prokaryote pan genome analysis

Cited by 3,813 publications

References 9 publications

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

Surveillance for Colonization, Transmission, and Infection With Methicillin-Susceptible Staphylococcus aureus in a Neonatal Intensive Care Unit

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