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Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite p...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592930/ https://www.ncbi.nlm.nih.gov/pubmed/28717047 http://dx.doi.org/10.1534/g3.117.043083 |
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author | Oldeschulte, David L. Halley, Yvette A. Wilson, Miranda L. Bhattarai, Eric K. Brashear, Wesley Hill, Joshua Metz, Richard P. Johnson, Charles D. Rollins, Dale Peterson, Markus J. Bickhart, Derek M. Decker, Jared E. Sewell, John F. Seabury, Christopher M. |
author_facet | Oldeschulte, David L. Halley, Yvette A. Wilson, Miranda L. Bhattarai, Eric K. Brashear, Wesley Hill, Joshua Metz, Richard P. Johnson, Charles D. Rollins, Dale Peterson, Markus J. Bickhart, Derek M. Decker, Jared E. Sewell, John F. Seabury, Christopher M. |
author_sort | Oldeschulte, David L. |
collection | PubMed |
description | Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15–20 KYA. |
format | Online Article Text |
id | pubmed-5592930 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-55929302017-09-14 Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size Oldeschulte, David L. Halley, Yvette A. Wilson, Miranda L. Bhattarai, Eric K. Brashear, Wesley Hill, Joshua Metz, Richard P. Johnson, Charles D. Rollins, Dale Peterson, Markus J. Bickhart, Derek M. Decker, Jared E. Sewell, John F. Seabury, Christopher M. G3 (Bethesda) Investigations Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15–20 KYA. Genetics Society of America 2017-07-17 /pmc/articles/PMC5592930/ /pubmed/28717047 http://dx.doi.org/10.1534/g3.117.043083 Text en Copyright © 2017 Oldeschulte et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article 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 the original work is properly cited. |
spellingShingle | Investigations Oldeschulte, David L. Halley, Yvette A. Wilson, Miranda L. Bhattarai, Eric K. Brashear, Wesley Hill, Joshua Metz, Richard P. Johnson, Charles D. Rollins, Dale Peterson, Markus J. Bickhart, Derek M. Decker, Jared E. Sewell, John F. Seabury, Christopher M. Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title | Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title_full | Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title_fullStr | Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title_full_unstemmed | Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title_short | Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size |
title_sort | annotated draft genome assemblies for the northern bobwhite (colinus virginianus) and the scaled quail (callipepla squamata) reveal disparate estimates of modern genome diversity and historic effective population size |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592930/ https://www.ncbi.nlm.nih.gov/pubmed/28717047 http://dx.doi.org/10.1534/g3.117.043083 |
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