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Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing

Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of...

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Autores principales: Chen, Chao, Parejo, Melanie, Momeni, Jamal, Langa, Jorge, Nielsen, Rasmus O., Shi, Wei, Vingborg, Rikke, Kryger, Per, Bouga, Maria, Estonba, Andone, Meixner, Marina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8872436/
https://www.ncbi.nlm.nih.gov/pubmed/35205227
http://dx.doi.org/10.3390/genes13020182
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author Chen, Chao
Parejo, Melanie
Momeni, Jamal
Langa, Jorge
Nielsen, Rasmus O.
Shi, Wei
Vingborg, Rikke
Kryger, Per
Bouga, Maria
Estonba, Andone
Meixner, Marina
author_facet Chen, Chao
Parejo, Melanie
Momeni, Jamal
Langa, Jorge
Nielsen, Rasmus O.
Shi, Wei
Vingborg, Rikke
Kryger, Per
Bouga, Maria
Estonba, Andone
Meixner, Marina
author_sort Chen, Chao
collection PubMed
description Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.
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spelling pubmed-88724362022-02-25 Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing Chen, Chao Parejo, Melanie Momeni, Jamal Langa, Jorge Nielsen, Rasmus O. Shi, Wei Vingborg, Rikke Kryger, Per Bouga, Maria Estonba, Andone Meixner, Marina Genes (Basel) Article Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory. MDPI 2022-01-21 /pmc/articles/PMC8872436/ /pubmed/35205227 http://dx.doi.org/10.3390/genes13020182 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chen, Chao
Parejo, Melanie
Momeni, Jamal
Langa, Jorge
Nielsen, Rasmus O.
Shi, Wei
Vingborg, Rikke
Kryger, Per
Bouga, Maria
Estonba, Andone
Meixner, Marina
Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title_full Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title_fullStr Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title_full_unstemmed Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title_short Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
title_sort population structure and diversity in european honey bees (apis mellifera l.)—an empirical comparison of pool and individual whole-genome sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8872436/
https://www.ncbi.nlm.nih.gov/pubmed/35205227
http://dx.doi.org/10.3390/genes13020182
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