April 23, 2009

Scientists Complete Cow Genome Sequence

Scientists from the University of Maryland have published a new version of the genome of the domestic cow, known as Bos Taurus, which considerably improves previous assemblies in terms of accuracy and totality.

The new cattle sequence took six years to complete, annotate and analyze and has involved over 300 scientists from 25 countries.

Sequencing of the bovine genome provides new information about mammalian evolution as well as cattle-specific biology, and points the way to research that could result in more sustainable food production in a world challenged by global population growth, said a consortium of researchers led by the Baylor College of Medicine Human Genome Sequencing Center in two reports that appear today in the journal Science.

The researchers, led by Steven Salzberg, developed customized software to assemble 35 million DNA sequence fragments into the 30 chromosomes that make up the Bos taurus genome. The algorithms use paired-end sequence information, mapping data, and synteny with the human genome to detect errors, correct inverted segments and fill in sequence gaps. The resulting assembly has around 91% of the assembled genome anchored onto chromosomes.

The researchers believe their assembly is the best available, thanks to the algorithm's ability to smooth out thousands of errors. 

Furthermore, comparisons demonstrate that the new cow genome assembly has better agreement with independent genetic maps, and a more complete representation of cow genes, than alternative assemblies.

The new assembly places some 150 million nucleotides (6%) more DNA sequence data onto chromosomes than the other draft assembly now available, known as BosTau4.0 from the Baylor College of Medicine.

A new, expanded cow-human synteny map increases the number of syntenic breakpoints by approximately 30%. Salzberg's team also identified a portion of the Bos taurus Y chromosome for the first time.

"Until the assembly is truly finished - a state that no mammalian genome, including human, has yet reached - we will continue to incorporate new data to fill in gaps, to correct the mis-oriented regions, and to place more sequences onto chromosomes," says Salzberg.

The alpaca and sheep genomes are currently being sequenced, and should provide a valuable source for making further improvements between these closely related mammals.

Although sequencing and assembly of mammalian genomes has become commonplace since the human genome was first sequenced seven years ago, assembling large genomes accurately remains a challenge.

"The future challenge will be to explore the bovine genome sequence in greater depth to fully understand the genetic basis of the evolutionary success of ruminants as this will provide opportunities to address some of the crucial issues of the present time "“ efficient and sustainable food production for a rapidly increasing human population," said Dr. Richard Gibbs, director of the BCM Human Genome Sequencing Center and a principal investigator on the project.

An article describing the research is freely available in BioMed Central's open access journal Genome Biology. The consortium has also published two reports that appear today in the journal Science.  Additionally, most of more than 25 companion reports describing detailed analyses of the projects appear online at www.biomedcentral.com in a special electronic issue of the BioMed Central journal.


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