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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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/6/847 |
| _version_ | 1797531987674660864 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T10:52:38Z |
| format | Article |
| id | doaj.art-63a7b305aff34e4d8fea627a299facad |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T10:52:38Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-63a7b305aff34e4d8fea627a299facad2023-11-21T22:08:05ZengMDPI AGGenes2073-44252021-05-0112684710.3390/genes12060847Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference GenomeVidhya Jagannathan0Christophe Hitte1Jeffrey M. Kidd2Patrick Masterson3Terence D. Murphy4Sarah Emery5Brian Davis6Reuben M. Buckley7Yan-Hu Liu8Xiang-Quan Zhang9Tosso Leeb10Ya-Ping Zhang11Elaine A. Ostrander12Guo-Dong Wang13Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001 Bern, SwitzerlandInstitute Genetics Development Rennes, University of Rennes, CNRS—UMR 6290, F-35000 Rennes, FranceDepartment of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USADepartment of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USADepartment of Integrative Biological Sciences, Texas A and M University, College Station, TX 77840, USANational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USAState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, ChinaState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, ChinaVetsuisse Faculty, Institute of Genetics, University of Bern, 3001 Bern, SwitzerlandState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, ChinaNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USAState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, ChinaThe 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.https://www.mdpi.com/2073-4425/12/6/847<i>Canis lupus familiaris</i>high qualitycontiguityPacific biosciencesannotationresource |
| spellingShingle | 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 Genes <i>Canis lupus familiaris</i> high quality contiguity Pacific biosciences annotation resource |
| title | 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_short | 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 |
| topic | <i>Canis lupus familiaris</i> high quality contiguity Pacific biosciences annotation resource |
| url | https://www.mdpi.com/2073-4425/12/6/847 |
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