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From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

BACKGROUND: Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference ge...

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Autores principales: Wright, Belinda, Farquharson, Katherine A., McLennan, Elspeth A., Belov, Katherine, Hogg, Carolyn J., Grueber, Catherine E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547446/
https://www.ncbi.nlm.nih.gov/pubmed/31159724
http://dx.doi.org/10.1186/s12864-019-5806-y
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author Wright, Belinda
Farquharson, Katherine A.
McLennan, Elspeth A.
Belov, Katherine
Hogg, Carolyn J.
Grueber, Catherine E.
author_facet Wright, Belinda
Farquharson, Katherine A.
McLennan, Elspeth A.
Belov, Katherine
Hogg, Carolyn J.
Grueber, Catherine E.
author_sort Wright, Belinda
collection PubMed
description BACKGROUND: Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes. RESULTS: Although we identified orders of magnitude fewer SNPs in our devil dataset than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data. CONCLUSIONS: For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAMtools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5806-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-65474462019-06-06 From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species Wright, Belinda Farquharson, Katherine A. McLennan, Elspeth A. Belov, Katherine Hogg, Carolyn J. Grueber, Catherine E. BMC Genomics Research Article BACKGROUND: Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes. RESULTS: Although we identified orders of magnitude fewer SNPs in our devil dataset than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data. CONCLUSIONS: For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAMtools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5806-y) contains supplementary material, which is available to authorized users. BioMed Central 2019-06-03 /pmc/articles/PMC6547446/ /pubmed/31159724 http://dx.doi.org/10.1186/s12864-019-5806-y Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Wright, Belinda
Farquharson, Katherine A.
McLennan, Elspeth A.
Belov, Katherine
Hogg, Carolyn J.
Grueber, Catherine E.
From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title_full From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title_fullStr From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title_full_unstemmed From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title_short From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
title_sort from reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547446/
https://www.ncbi.nlm.nih.gov/pubmed/31159724
http://dx.doi.org/10.1186/s12864-019-5806-y
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