The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies
Abstract Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like...
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Oxford University Press (OUP)
2024
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Online Access: | http://dx.doi.org/10.1093/jhered/esae013 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esae013/57141076/esae013.pdf https://academic.oup.com/jhered/article-pdf/115/4/480/58498589/esae013.pdf |
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croxfordunivpr:10.1093/jhered/esae013 2024-10-20T14:08:56+00:00 The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies Bredemeyer, Kevin R vonHoldt, Bridgett M Foley, Nicole M Childers, Isabella R Brzeski, Kristin E Murphy, William J Shapiro, Beth U.S. Fish & Wildlife Service U.S. National Science Foundation 2024 http://dx.doi.org/10.1093/jhered/esae013 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esae013/57141076/esae013.pdf https://academic.oup.com/jhered/article-pdf/115/4/480/58498589/esae013.pdf en eng Oxford University Press (OUP) https://academic.oup.com/pages/standard-publication-reuse-rights Journal of Heredity volume 115, issue 4, page 480-486 ISSN 0022-1503 1465-7333 journal-article 2024 croxfordunivpr https://doi.org/10.1093/jhered/esae013 2024-09-24T04:08:06Z Abstract Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics. Article in Journal/Newspaper gray wolf Oxford University Press Journal of Heredity |
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Open Polar |
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Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
Abstract Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics. |
author2 |
Shapiro, Beth U.S. Fish & Wildlife Service U.S. National Science Foundation |
format |
Article in Journal/Newspaper |
author |
Bredemeyer, Kevin R vonHoldt, Bridgett M Foley, Nicole M Childers, Isabella R Brzeski, Kristin E Murphy, William J |
spellingShingle |
Bredemeyer, Kevin R vonHoldt, Bridgett M Foley, Nicole M Childers, Isabella R Brzeski, Kristin E Murphy, William J The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
author_facet |
Bredemeyer, Kevin R vonHoldt, Bridgett M Foley, Nicole M Childers, Isabella R Brzeski, Kristin E Murphy, William J |
author_sort |
Bredemeyer, Kevin R |
title |
The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
title_short |
The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
title_full |
The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
title_fullStr |
The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
title_full_unstemmed |
The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies |
title_sort |
value of hybrid genomes: building two highly contiguous reference genome assemblies to advance canis genomic studies |
publisher |
Oxford University Press (OUP) |
publishDate |
2024 |
url |
http://dx.doi.org/10.1093/jhered/esae013 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esae013/57141076/esae013.pdf https://academic.oup.com/jhered/article-pdf/115/4/480/58498589/esae013.pdf |
genre |
gray wolf |
genre_facet |
gray wolf |
op_source |
Journal of Heredity volume 115, issue 4, page 480-486 ISSN 0022-1503 1465-7333 |
op_rights |
https://academic.oup.com/pages/standard-publication-reuse-rights |
op_doi |
https://doi.org/10.1093/jhered/esae013 |
container_title |
Journal of Heredity |
_version_ |
1813448150256451584 |