Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |
_version_ | 1784657238313402368 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8872436 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT chenchao populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT parejomelanie populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT momenijamal populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT langajorge populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT nielsenrasmuso populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT shiwei populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT vingborgrikke populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT krygerper populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT bougamaria populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT estonbaandone populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing AT meixnermarina populationstructureanddiversityineuropeanhoneybeesapismelliferalanempiricalcomparisonofpoolandindividualwholegenomesequencing |