Publication:
GenomegaMap: Within-Species Genome-Wide d<inf>N</inf>=d<inf>S</inf> Estimation from over 10,000 Genomes

Issued Date

2021-01-01

Resource Type

Article

ISSN

15371719
07374038

DOI

10.1093/MOLBEV/MSAA069

Other identifier(s)

2-s2.0-85089203677

Rights

Mahidol University

Rights Holder(s)

SCOPUS

Bibliographic Citation

Molecular Biology and Evolution. Vol.37, No.8 (2021), 2450-2460

Suggested Citation

Daniel J. Wilson, Derrick W. Crook, Timothy E.A. Peto, A. Sarah Walker, Sarah J. Hoosdally, Ana L. Gibertoni Cruz, Joshua Carter, Clara Grazian, Sarah G. Earle, Samaneh Kouchaki, Alexander Lachapelle, Yang Yang, David A. Clifton, Philip W. Fowler, Zamin Iqbal, Martin Hunt, Jeffrey Knaggs, E. Grace Smith, Priti Rathod, Lisa Jarrett, Daniela Matias, Daniela M. Cirillo, Emanuele Borroni, Simone Battaglia, Arash Ghodousi, Andrea Spitaleri, Andrea Cabibbe, Sabira Tahseen, Kayzad Nilgiriwala, Sanchi Shah, Camilla Rodrigues, Priti Kambli, Utkarsha Surve, Rukhsar Khot, Stefan Niemann, Thomas A. Kohl, Matthias Merker, Harald Hoffmann, Katharina Todt, Sara Plesnik, Nazir Ismail, Shaheed Vally Omar, Lavania Joseph, Guy Thwaites, Thuong Nguyen Thuy Thuong, Nhung Hoang Ngoc, Vijay Srinivasan, Timothy M. Walker, David Moore, Jorge Coronel, Walter Solano, George F. Gao, Guangxue He, Yanlin Zhao, Chunfa Liu, Aijing Ma, Baoli Zhu, Ian Laurenson, Pauline Claxton, Anastasia Koch, Robert Wilkinson, Ajit Lalvani, James Posey, Jennifer Gardy, Jim Werngren, Nicholas Paton, Ruwen Jou, Mei Hua Wu, Wan Hsuan Lin, Lucilaine Ferrazoli, Rosangela Siqueira de Oliveira, Irena Arandjelovic, Angkana Chaiprasert, Inaki Comas, Francis A. Drobniewski, Maha R. Farhat, Qian Gao, Rick Ong Twee Hee, Vitali Sintchenko, Philip Supply, Dick van Soolingen GenomegaMap: Within-Species Genome-Wide d<inf>N</inf>=d<inf>S</inf> Estimation from over 10,000 Genomes. Molecular Biology and Evolution. Vol.37, No.8 (2021), 2450-2460. doi:10.1093/MOLBEV/MSAA069 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/75819

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Title

GenomegaMap: Within-Species Genome-Wide d<inf>N</inf>=d<inf>S</inf> Estimation from over 10,000 Genomes

Author(s)

Daniel J. Wilson
 Derrick W. Crook
 Timothy E.A. Peto
 A. Sarah Walker
 Sarah J. Hoosdally
 Ana L. Gibertoni Cruz
 Joshua Carter
 Clara Grazian
 Sarah G. Earle
 Samaneh Kouchaki
 Alexander Lachapelle
 Yang Yang
 David A. Clifton
 Philip W. Fowler
 Zamin Iqbal
 Martin Hunt
 Jeffrey Knaggs
 E. Grace Smith
 Priti Rathod
 Lisa Jarrett
 Daniela Matias
 Daniela M. Cirillo
 Emanuele Borroni
 Simone Battaglia
 Arash Ghodousi
 Andrea Spitaleri
 Andrea Cabibbe
 Sabira Tahseen
 Kayzad Nilgiriwala
 Sanchi Shah
 Camilla Rodrigues
 Priti Kambli
 Utkarsha Surve
 Rukhsar Khot
 Stefan Niemann
 Thomas A. Kohl
 Matthias Merker
 Harald Hoffmann
 Katharina Todt
 Sara Plesnik
 Nazir Ismail
 Shaheed Vally Omar
 Lavania Joseph
 Guy Thwaites
 Thuong Nguyen Thuy Thuong
 Nhung Hoang Ngoc
 Vijay Srinivasan
 Timothy M. Walker
 David Moore
 Jorge Coronel
 Walter Solano
 George F. Gao
 Guangxue He
 Yanlin Zhao
 Chunfa Liu
 Aijing Ma
 Baoli Zhu
 Ian Laurenson
 Pauline Claxton
 Anastasia Koch
 Robert Wilkinson
 Ajit Lalvani
 James Posey
 Jennifer Gardy
 Jim Werngren
 Nicholas Paton
 Ruwen Jou
 Mei Hua Wu
 Wan Hsuan Lin
 Lucilaine Ferrazoli
 Rosangela Siqueira de Oliveira
 Irena Arandjelovic
 Angkana Chaiprasert
 Inaki Comas
 Francis A. Drobniewski
 Maha R. Farhat
 Qian Gao
 Rick Ong Twee Hee
 Vitali Sintchenko
 Philip Supply
 Dick van Soolingen

Other Contributor(s)

Siriraj Hospital
 Public Health Agency of Sweden
 Oxford University Clinical Research Unit
 Second Affiliated Hospital of Southern University of Science and Technology
 Public Health England
 Université de Lille
 Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
 Forschungszentrum Borstel - Zentrum für Medizin und Biowissenschaften
 Belgrade University School of Medicine
 The Foundation for Medical Research India
 CSIC - Instituto de Biomedicina de Valencia (IBV)
 National Institute for Communicable Diseases
 London School of Hygiene &amp; Tropical Medicine
 Instituto Adolfo Lutz
 University of Oxford
 National Institute for Public Health and the Environment
 European Bioinformatics Institute
 The University of Sydney
 IRCCS Ospedale San Raffaele
 Asklepios Fachkliniken München-Gauting
 P.D. Hinduja National Hospital and Medical Research Centre
 Centers for Disease Control and Prevention
 Institute of Microbiology Chinese Academy of Sciences
 National University of Singapore
 Imperial College London
 The University of British Columbia
 Fudan University
 Nuffield Department of Medicine
 Harvard Medical School
 University of Cape Town
 Universidad Peruana Cayetano Hereda
 CDC Taiwan
 FISABIO-Public Health
 National Tuberculosis Control Program Pakistan
 Scottish Mycobacteria Reference Laboratory
 China CDC

Abstract

The dN=dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN=dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN=dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap's simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.

Keyword(s)

Agricultural and Biological Sciences
 Biochemistry, Genetics and Molecular Biology

Availability

URI

https://repository.li.mahidol.ac.th/handle/20.500.14594/75819

Collections

Scopus 2021