Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource
2021
Аутори:
Kapun, MartinNunez, Joaquin C B
Bogaerts-Márquez, María
Murga-Moreno, Jesús
Paris, Margot
Outten, Joseph
Coronado-Zamora, Marta
Tern, Courtney
Rota-Stabelli, Omar
Guerreiro, Maria P García
Casillas, Sònia
Orengo, Dorcas J
Puerma, Eva
Kankare, Maaria
Ometto, Lino
Loeschcke, Volker
Onder, Banu S
Abbott, Jessica K
Schaeffer, Stephen W
Rajpurohit, Subhash
Behrman, Emily L
Schou, Mads F
Merritt, Thomas J S
Lazzaro, Brian P
Glaser-Schmitt, Amanda
Argyridou, Eliza
Staubach, Fabian
Wang, Yun
Tauber, Eran
Serga, Svitlana V
Fabian, Daniel K
Dyer, Kelly A
Wheat, Christopher W
Parsch, John
Grath, Sonja
Savić Veselinović, Marija
Stamenković-Radak, Marina
Jelić, Mihailo
Buendía-Ruíz, Antonio J
Gómez-Julián, Maria Josefa
Espinosa-Jimenez, Maria Luisa
Gallardo-Jiménez, Francisco D
Patenković, Aleksandra
Erić, Katarina
Tanasković, Marija
Ullastres, Anna
Guio, Lain
Merenciano, Miriam
Guirao-Rico, Sara
Horváth, Vivien
Obbard, Darren J
Pasyukova, Elena
Alatortsev, Vladimir E
Vieira, Cristina P
Vieira, Jorge
Torres, Jorge Roberto
Kozeretska, Iryna
Maistrenko, Oleksandr M
Montchamp-Moreau, Catherine
Mukha, Dmitry V
Machado, Heather E
Lamb, Keric
Paulo, Tânia
Yusuf, Leeban
Barbadilla, Antonio
Petrov, Dmitri
Schmidt, Paul
Gonzalez, Josefa
Flatt, Thomas
Bergland, Alan O
Nielsen, Rasmus
Тип документа:
Чланак у часопису (Објављена верзија)
,
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Метаподаци
Приказ свих података о документуАпстракт:
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.
Кључне речи:
Drosophila melanogaster; Population genomics; SNPs; Evolution; Adaptation; DemographyИзвор:
Molecular Biology and Evolution, 2021, 38, 12, 5782-5805Финансирање / пројекти:
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200007 (Универзитет у Београду, Институт за биолошка истраживања 'Синиша Станковић') (RS-MESTD-inst-2020-200007)
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200178 (Универзитет у Београду, Биолошки факултет) (RS-MESTD-inst-2020-200178)
- Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB)
- Austrian Science Fund (FWF)
- European Research Council (ERC)
- Spanish Government
- Swiss National Science Foundation (SNSF)
- German Research Foundation (DFG)
- Danish Natural Science Research Council
- United States Department of Health & Human Services National Institutes of Health (NIH) - USA
- Israel Science Foundation
- Natural Sciences and Engineering Research Council of Canada (NSERC)
DOI: 10.1093/molbev/msab259
ISSN: 0737-4038
PubMed: 34469576
WoS: 000741368600039
[ Google Scholar ]URI
https://academic.oup.com/mbe/article/38/12/5782/6361628http://radar.ibiss.bg.ac.rs/handle/123456789/4765