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Bos taurus genome assembly
BACKGROUND: We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS: The assembly process...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686734/ https://www.ncbi.nlm.nih.gov/pubmed/19393050 http://dx.doi.org/10.1186/1471-2164-10-180 |
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author | Liu, Yue Qin, Xiang Song, Xing-Zhi Henry Jiang, Huaiyang Shen, Yufeng Durbin, K James Lien, Sigbjørn Kent, Matthew Peter Sodeland, Marte Ren, Yanru Zhang, Lan Sodergren, Erica Havlak, Paul Worley, Kim C Weinstock, George M Gibbs, Richard A |
author_facet | Liu, Yue Qin, Xiang Song, Xing-Zhi Henry Jiang, Huaiyang Shen, Yufeng Durbin, K James Lien, Sigbjørn Kent, Matthew Peter Sodeland, Marte Ren, Yanru Zhang, Lan Sodergren, Erica Havlak, Paul Worley, Kim C Weinstock, George M Gibbs, Richard A |
author_sort | Liu, Yue |
collection | PubMed |
description | BACKGROUND: We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS: The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. CONCLUSION: The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research. |
format | Text |
id | pubmed-2686734 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26867342009-05-27 Bos taurus genome assembly Liu, Yue Qin, Xiang Song, Xing-Zhi Henry Jiang, Huaiyang Shen, Yufeng Durbin, K James Lien, Sigbjørn Kent, Matthew Peter Sodeland, Marte Ren, Yanru Zhang, Lan Sodergren, Erica Havlak, Paul Worley, Kim C Weinstock, George M Gibbs, Richard A BMC Genomics Research Article BACKGROUND: We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS: The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. CONCLUSION: The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research. BioMed Central 2009-04-24 /pmc/articles/PMC2686734/ /pubmed/19393050 http://dx.doi.org/10.1186/1471-2164-10-180 Text en Copyright © 2009 Liu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Liu, Yue Qin, Xiang Song, Xing-Zhi Henry Jiang, Huaiyang Shen, Yufeng Durbin, K James Lien, Sigbjørn Kent, Matthew Peter Sodeland, Marte Ren, Yanru Zhang, Lan Sodergren, Erica Havlak, Paul Worley, Kim C Weinstock, George M Gibbs, Richard A Bos taurus genome assembly |
title | Bos taurus genome assembly |
title_full | Bos taurus genome assembly |
title_fullStr | Bos taurus genome assembly |
title_full_unstemmed | Bos taurus genome assembly |
title_short | Bos taurus genome assembly |
title_sort | bos taurus genome assembly |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686734/ https://www.ncbi.nlm.nih.gov/pubmed/19393050 http://dx.doi.org/10.1186/1471-2164-10-180 |
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