This article is part of a series on Bovine: the companion papers for the publication of the bovine genome sequence.

Research article

Bos taurus genome assembly

Yue Liu¹ , Xiang Qin¹ , Xing-Zhi Henry Song¹ , Huaiyang Jiang¹ , Yufeng Shen^1,2 , K James Durbin^1,3 , Sigbjørn Lien⁴ , Matthew Peter Kent⁴ , Marte Sodeland⁴ , Yanru Ren¹ , Lan Zhang¹ , Erica Sodergren^1,5 , Paul Havlak^1,6 , Kim C Worley¹ , George M Weinstock^1,5 and Richard A Gibbs¹

¹Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA

²Department of Computer Science and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA

³Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA

⁴Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, Ås, 1432, Norway

⁵Washington University St Louis, MO, USA

⁶Department of Computer Science, University of Houston, 4800 Calhoun Road, Houston, TX 77204-3010, USA

author email corresponding author email

BMC Genomics 2009, 10:180doi:10.1186/1471-2164-10-180

Published:	24 April 2009

Abstract

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.