Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome
The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sa...
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Online Access: | https://doi.org/10.3390/genes12060847 |
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ftmdpi:oai:mdpi.com:/2073-4425/12/6/847/ 2023-08-20T04:05:47+02:00 Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome Vidhya Jagannathan Christophe Hitte Jeffrey M. Kidd Patrick Masterson Terence D. Murphy Sarah Emery Brian Davis Reuben M. Buckley Yan-Hu Liu Xiang-Quan Zhang Tosso Leeb Ya-Ping Zhang Elaine A. Ostrander Guo-Dong Wang agris 2021-05-30 application/pdf https://doi.org/10.3390/genes12060847 EN eng Multidisciplinary Digital Publishing Institute Animal Genetics and Genomics https://dx.doi.org/10.3390/genes12060847 https://creativecommons.org/licenses/by/4.0/ Genes; Volume 12; Issue 6; Pages: 847 Canis lupus familiaris high quality contiguity Pacific biosciences annotation resource Text 2021 ftmdpi https://doi.org/10.3390/genes12060847 2023-08-01T01:50:46Z The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5. Text Canis lupus MDPI Open Access Publishing Pacific Genes 12 6 847 |
institution |
Open Polar |
collection |
MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
Canis lupus familiaris high quality contiguity Pacific biosciences annotation resource |
spellingShingle |
Canis lupus familiaris high quality contiguity Pacific biosciences annotation resource Vidhya Jagannathan Christophe Hitte Jeffrey M. Kidd Patrick Masterson Terence D. Murphy Sarah Emery Brian Davis Reuben M. Buckley Yan-Hu Liu Xiang-Quan Zhang Tosso Leeb Ya-Ping Zhang Elaine A. Ostrander Guo-Dong Wang Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
topic_facet |
Canis lupus familiaris high quality contiguity Pacific biosciences annotation resource |
description |
The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5. |
format |
Text |
author |
Vidhya Jagannathan Christophe Hitte Jeffrey M. Kidd Patrick Masterson Terence D. Murphy Sarah Emery Brian Davis Reuben M. Buckley Yan-Hu Liu Xiang-Quan Zhang Tosso Leeb Ya-Ping Zhang Elaine A. Ostrander Guo-Dong Wang |
author_facet |
Vidhya Jagannathan Christophe Hitte Jeffrey M. Kidd Patrick Masterson Terence D. Murphy Sarah Emery Brian Davis Reuben M. Buckley Yan-Hu Liu Xiang-Quan Zhang Tosso Leeb Ya-Ping Zhang Elaine A. Ostrander Guo-Dong Wang |
author_sort |
Vidhya Jagannathan |
title |
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
title_short |
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
title_full |
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
title_fullStr |
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
title_full_unstemmed |
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome |
title_sort |
dog10k_boxer_tasha_1.0: a long-read assembly of the dog reference genome |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2021 |
url |
https://doi.org/10.3390/genes12060847 |
op_coverage |
agris |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Genes; Volume 12; Issue 6; Pages: 847 |
op_relation |
Animal Genetics and Genomics https://dx.doi.org/10.3390/genes12060847 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/genes12060847 |
container_title |
Genes |
container_volume |
12 |
container_issue |
6 |
container_start_page |
847 |
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1774716520992079872 |