Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A., Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10 (4). ISSN 14747596 (ISSN)
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Abstract
Background: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods. Results: We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions. Conclusions: By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome. © 2009 Zimin et al.; licensee BioMed Central Ltd.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | accuracy animal genetics article base pairing chromosome analysis controlled study cow domestic animal gene deletion gene mapping gene translocation genetic conservation genome analysis haplotype map human human genome nonhuman sequence alignment sequence analysis single nucleotide polymorphism synteny Y chromosome animal cattle chromosome map DNA sequence female genetics genome genomics male methodology statistics Bos taurus Animals Chromosome Mapping Genome, Human Humans Sequence Analysis, DNA |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > animal bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 2009 |
| Date Deposited: | 15 Mar 2013 18:03 |
| Last Modified: | 15 Mar 2013 18:03 |
| PMCID: | PMC2688933 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27838 |
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