Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Martin Kapun; Joaquin C.B. Nunez; María Bogaerts-Márquez; Jesús Murga-Moreno; Margot Paris; Joseph Outten; Marta Coronado-Zamora; Courtney Tern; Omar Rota-Stabelli; Maria P. García Guerreiro; Sònia Casillas; Dorcas J. Orengo; Eva Puerma; Maaria Kankare; Lino Ometto; Volker Loeschcke; Banu S. Onder; Jessica K. Abbott; Stephen W. Schaeffer; Subhash Rajpurohit; Emily L. Behrman; Mads F. Schou; Thomas J.S. Merritt; Brian P. Lazzaro; Amanda Glaser-Schmitt; Eliza Argyridou; Fabian Staubach; Yun Wang; Eran Tauber; Svitlana V. Serga; Daniel K. Fabian; Kelly A. Dyer; Christopher W. Wheat; John Parsch; Sonja Grath; Marija Savic Veselinovic; Marina Stamenkovic-Radak; Mihailo Jelic; Antonio J. Buendía-Ruíz; Maria Josefa Gómez-Julián; Maria Luisa Espinosa-Jimenez; Francisco D. Gallardo-Jiménez; Aleksandra Patenkovic; Katarina Eric; Marija Tanaskovic; Anna Ullastres; Lain Guio; Miriam Merenciano; Sara Guirao-Rico; Vivien Horváth

doi:10.1093/molbev/msab259

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Martin Kapun^*, Joaquin C.B. Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. García Guerreiro, Sònia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash RajpurohitEmily L. Behrman, Mads F. Schou, Thomas J.S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana V. Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendía-Ruíz, Maria Josefa Gómez-Julián, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jiménez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horváth

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

30 Citationer (Scopus)

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

Originalsprog	Engelsk
Tidsskrift	Molecular Biology and Evolution
Vol/bind	38
Nummer	12
Sider (fra-til)	5782-5805
Antal sider	24
ISSN	0737-4038
DOI	https://doi.org/10.1093/molbev/msab259
Status	Udgivet - 2021

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Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., García Guerreiro, M. P., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., ... Horváth, V. (2021). Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Molecular Biology and Evolution, 38(12), 5782-5805. https://doi.org/10.1093/molbev/msab259

@article{9a2cf5f7dbd14b17b9553fd31fea58f7,

title = "Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource",

abstract = "Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.",

keywords = "Adaptation, Demography, Drosophila melanogaster, Evolution, Population genomics, SNPs",

author = "Martin Kapun and Nunez, {Joaquin C.B.} and Mar{\'i}a Bogaerts-M{\'a}rquez and Jes{\'u}s Murga-Moreno and Margot Paris and Joseph Outten and Marta Coronado-Zamora and Courtney Tern and Omar Rota-Stabelli and {Garc{\'i}a Guerreiro}, {Maria P.} and S{\`o}nia Casillas and Orengo, {Dorcas J.} and Eva Puerma and Maaria Kankare and Lino Ometto and Volker Loeschcke and Onder, {Banu S.} and Abbott, {Jessica K.} and Schaeffer, {Stephen W.} and Subhash Rajpurohit and Behrman, {Emily L.} and Schou, {Mads F.} and Merritt, {Thomas J.S.} and Lazzaro, {Brian P.} and Amanda Glaser-Schmitt and Eliza Argyridou and Fabian Staubach and Yun Wang and Eran Tauber and Serga, {Svitlana V.} and Fabian, {Daniel K.} and Dyer, {Kelly A.} and Wheat, {Christopher W.} and John Parsch and Sonja Grath and Veselinovic, {Marija Savic} and Marina Stamenkovic-Radak and Mihailo Jelic and Buend{\'i}a-Ru{\'i}z, {Antonio J.} and G{\'o}mez-Juli{\'a}n, {Maria Josefa} and Espinosa-Jimenez, {Maria Luisa} and Gallardo-Jim{\'e}nez, {Francisco D.} and Aleksandra Patenkovic and Katarina Eric and Marija Tanaskovic and Anna Ullastres and Lain Guio and Miriam Merenciano and Sara Guirao-Rico and Vivien Horv{\'a}th",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2021.",

year = "2021",

doi = "10.1093/molbev/msab259",

language = "English",

volume = "38",

pages = "5782--5805",

journal = "Molecular Biology and Evolution",

issn = "0737-4038",

publisher = "Oxford University Press",

number = "12",

}

Kapun, M, Nunez, JCB, Bogaerts-Márquez, M, Murga-Moreno, J, Paris, M, Outten, J, Coronado-Zamora, M, Tern, C, Rota-Stabelli, O, García Guerreiro, MP, Casillas, S, Orengo, DJ, Puerma, E, Kankare, M, Ometto, L, Loeschcke, V, Onder, BS, Abbott, JK, Schaeffer, SW, Rajpurohit, S, Behrman, EL, Schou, MF, Merritt, TJS, Lazzaro, BP, Glaser-Schmitt, A, Argyridou, E, Staubach, F, Wang, Y, Tauber, E, Serga, SV, Fabian, DK, Dyer, KA, Wheat, CW, Parsch, J, Grath, S, Veselinovic, MS, Stamenkovic-Radak, M, Jelic, M, Buendía-Ruíz, AJ, Gómez-Julián, MJ, Espinosa-Jimenez, ML, Gallardo-Jiménez, FD, Patenkovic, A, Eric, K, Tanaskovic, M, Ullastres, A, Guio, L, Merenciano, M, Guirao-Rico, S & Horváth, V 2021, 'Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource', Molecular Biology and Evolution, bind 38, nr. 12, s. 5782-5805. https://doi.org/10.1093/molbev/msab259

TY - JOUR

T1 - Drosophila Evolution over Space and Time (DEST)

T2 - A New Population Genomics Resource

AU - Kapun, Martin

AU - Nunez, Joaquin C.B.

AU - Bogaerts-Márquez, María

AU - Murga-Moreno, Jesús

AU - Paris, Margot

AU - Outten, Joseph

AU - Coronado-Zamora, Marta

AU - Tern, Courtney

AU - Rota-Stabelli, Omar

AU - García Guerreiro, Maria P.

AU - Casillas, Sònia

AU - Orengo, Dorcas J.

AU - Puerma, Eva

AU - Kankare, Maaria

AU - Ometto, Lino

AU - Loeschcke, Volker

AU - Onder, Banu S.

AU - Abbott, Jessica K.

AU - Schaeffer, Stephen W.

AU - Rajpurohit, Subhash

AU - Behrman, Emily L.

AU - Schou, Mads F.

AU - Merritt, Thomas J.S.

AU - Lazzaro, Brian P.

AU - Glaser-Schmitt, Amanda

AU - Argyridou, Eliza

AU - Staubach, Fabian

AU - Wang, Yun

AU - Tauber, Eran

AU - Serga, Svitlana V.

AU - Fabian, Daniel K.

AU - Dyer, Kelly A.

AU - Wheat, Christopher W.

AU - Parsch, John

AU - Grath, Sonja

AU - Veselinovic, Marija Savic

AU - Stamenkovic-Radak, Marina

AU - Jelic, Mihailo

AU - Buendía-Ruíz, Antonio J.

AU - Gómez-Julián, Maria Josefa

AU - Espinosa-Jimenez, Maria Luisa

AU - Gallardo-Jiménez, Francisco D.

AU - Patenkovic, Aleksandra

AU - Eric, Katarina

AU - Tanaskovic, Marija

AU - Ullastres, Anna

AU - Guio, Lain

AU - Merenciano, Miriam

AU - Guirao-Rico, Sara

AU - Horváth, Vivien

PY - 2021

Y1 - 2021

N2 - Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

AB - Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

KW - Adaptation

KW - Demography

KW - Drosophila melanogaster

KW - Evolution

KW - Population genomics

KW - SNPs

UR - http://www.scopus.com/inward/record.url?scp=85123463299&partnerID=8YFLogxK

U2 - 10.1093/molbev/msab259

DO - 10.1093/molbev/msab259

M3 - Journal article

C2 - 34469576

AN - SCOPUS:85123463299

SN - 0737-4038

VL - 38

SP - 5782

EP - 5805

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 12

ER -

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

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