Estimating Pangenomes with Roary

Overview

Journal Mol Biol Evol

Publisher Oxford University Press

Specialty Biology

Date 2019 Dec 19

PMID 31848603

Citations 31

Authors

Farrah Sitto

Fabia U Battistuzzi

Affiliations

Soon will be listed here.

Abstract

A description of the genetic makeup of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides 1) an overview about core and accessory genes for those interested in general trends and, also, 2) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.

Citing Articles

Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes.

Nagy N, Hodor P PLoS One. 2024; 19(10):e0311520.

PMID: 39365807 PMC: 11452038. DOI: 10.1371/journal.pone.0311520.

Microevolution of driven by geographic and host factors.

Xu A, Lu L, Zhang W, Song X, Li G, Miao Y mSystems. 2024; 9(10):e0108924.

PMID: 39345150 PMC: 11494883. DOI: 10.1128/msystems.01089-24.

Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage.

Zheng X, Wang X, Zhou Y, Liu M, Li P, Gao L Arch Microbiol. 2024; 206(7):335.

PMID: 38953983 DOI: 10.1007/s00203-024-04061-w.

Genomic investigation of Salmonella enterica Serovar Welikade from a pediatric diarrhea case first time in Shanghai, China.

Shen Y, Zhou Y, Gong J, Li G, Liu Y, Xu X BMC Genomics. 2024; 25(1):604.

PMID: 38886668 PMC: 11181664. DOI: 10.1186/s12864-024-10489-7.

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity.

Tian X, Teo W, Yang Y, Dong L, Wong A, Chen L BMC Microbiol. 2024; 24(1):185.

PMID: 38802738 PMC: 11131293. DOI: 10.1186/s12866-024-03346-w.

References

Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J . PGAP: pan-genomes analysis pipeline. Bioinformatics. 2011; 28(3):416-8. PMC: 3268234. DOI: 10.1093/bioinformatics/btr655. View

Muzzi A, Donati C . Population genetics and evolution of the pan-genome of Streptococcus pneumoniae. Int J Med Microbiol. 2011; 301(8):619-22. DOI: 10.1016/j.ijmm.2011.09.008. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Page A, Cummins C, Hunt M, Wong V, Reuter S, Holden M . Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015; 31(22):3691-3. PMC: 4817141. DOI: 10.1093/bioinformatics/btv421. View

Contreras-Moreira B, Vinuesa P . GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013; 79(24):7696-701. PMC: 3837814. DOI: 10.1128/AEM.02411-13. View

Vernikos G, Medini D, Riley D, Tettelin H . Ten years of pan-genome analyses. Curr Opin Microbiol. 2014; 23:148-54. DOI: 10.1016/j.mib.2014.11.016. View

Moldovan M, Gelfand M . Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of spp. Front Microbiol. 2018; 9:428. PMC: 5857598. DOI: 10.3389/fmicb.2018.00428. View

Eggertsson H, Jonsson H, Kristmundsdottir S, Hjartarson E, Kehr B, Masson G . Graphtyper enables population-scale genotyping using pangenome graphs. Nat Genet. 2017; 49(11):1654-1660. DOI: 10.1038/ng.3964. View

Rodriguez-Valera F, Ussery D . Is the pan-genome also a pan-selectome?. F1000Res. 2013; 1:16. PMC: 3782348. DOI: 10.12688/f1000research.1-16.v1. View

10.

Ding W, Baumdicker F, Neher R . panX: pan-genome analysis and exploration. Nucleic Acids Res. 2017; 46(1):e5. PMC: 5758898. DOI: 10.1093/nar/gkx977. View

11.

Abreo E, Altier N . Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them. Sci Rep. 2019; 9(1):46. PMC: 6328595. DOI: 10.1038/s41598-018-37118-0. View

12.

Brynildsrud O, Bohlin J, Scheffer L, Eldholm V . Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 2016; 17(1):238. PMC: 5124306. DOI: 10.1186/s13059-016-1108-8. View

13.

Sheikhizadeh S, Schranz M, Akdel M, de Ridder D, Smit S . PanTools: representation, storage and exploration of pan-genomic data. Bioinformatics. 2016; 32(17):i487-i493. DOI: 10.1093/bioinformatics/btw455. View

14.

Nguyen N, Hickey G, Zerbino D, Raney B, Earl D, Armstrong J . Building a pan-genome reference for a population. J Comput Biol. 2015; 22(5):387-401. PMC: 4424974. DOI: 10.1089/cmb.2014.0146. View

15.

Tettelin H, Masignani V, Cieslewicz M, Donati C, Medini D, Ward N . Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005; 102(39):13950-5. PMC: 1216834. DOI: 10.1073/pnas.0506758102. View

16.

Locey K, Lennon J . Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A. 2016; 113(21):5970-5. PMC: 4889364. DOI: 10.1073/pnas.1521291113. View

17.

Tettelin H, Riley D, Cattuto C, Medini D . Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008; 11(5):472-7. DOI: 10.1016/j.mib.2008.09.006. View

18.

Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X . PGAP-X: extension on pan-genome analysis pipeline. BMC Genomics. 2018; 19(Suppl 1):36. PMC: 5780747. DOI: 10.1186/s12864-017-4337-7. View

19.

Bobay L, Ochman H . Biological species are universal across Life's domains. Genome Biol Evol. 2017; . PMC: 5381558. DOI: 10.1093/gbe/evx026. View

20.

McInerney J, McNally A, OConnell M . Why prokaryotes have pangenomes. Nat Microbiol. 2017; 2:17040. DOI: 10.1038/nmicrobiol.2017.40. View