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Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications

BACKGROUND: Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequ...

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Autores principales: Grogan, Kathleen E., McGinnis, Gwendolyn J., Sauther, Michelle L., Cuozzo, Frank P., Drea, Christine M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782575/
https://www.ncbi.nlm.nih.gov/pubmed/26957424
http://dx.doi.org/10.1186/s12864-016-2503-y
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author Grogan, Kathleen E.
McGinnis, Gwendolyn J.
Sauther, Michelle L.
Cuozzo, Frank P.
Drea, Christine M.
author_facet Grogan, Kathleen E.
McGinnis, Gwendolyn J.
Sauther, Michelle L.
Cuozzo, Frank P.
Drea, Christine M.
author_sort Grogan, Kathleen E.
collection PubMed
description BACKGROUND: Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes. RESULTS: In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1–7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies. CONCLUSIONS: In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2503-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-47825752016-03-09 Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications Grogan, Kathleen E. McGinnis, Gwendolyn J. Sauther, Michelle L. Cuozzo, Frank P. Drea, Christine M. BMC Genomics Research Article BACKGROUND: Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes. RESULTS: In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1–7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies. CONCLUSIONS: In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2503-y) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-08 /pmc/articles/PMC4782575/ /pubmed/26957424 http://dx.doi.org/10.1186/s12864-016-2503-y Text en © Grogan et al. 2016 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
Grogan, Kathleen E.
McGinnis, Gwendolyn J.
Sauther, Michelle L.
Cuozzo, Frank P.
Drea, Christine M.
Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title_full Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title_fullStr Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title_full_unstemmed Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title_short Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
title_sort next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782575/
https://www.ncbi.nlm.nih.gov/pubmed/26957424
http://dx.doi.org/10.1186/s12864-016-2503-y
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