Abstract
BackgroundWe 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.ResultsThe 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.ConclusionThe biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.
Highlights
We present here the assembly of the bovine genome
The bovine genome was assembled at the Baylor College of Medicine Human Genome Sequencing Center using a combined method similar to that used for the rat genome[9] and more recently the sea urchin genome[8]
The combined strategy is a hybrid of the Whole Genome Shotgun (WGS) approach used for the mouse genome and the hierarchical (BAC clone) approach used for the human genome
Summary
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. Methods are chosen that can be applied to the entire genome for a consistent result. The sequences can be aggressively merged creating false joins in some cases but at the same time producing a statistically more contiguous assembly. The human genome[1] was assembled using a hierarchical approach, where bacterial artificial chromosomes (BACs) were isolated and mapped to the genome and individually sequenced. The advantage of this method is that the individual BACs contain a single haplotype and the assembly within a BAC avoids conflicts due to polymorphisms and as a result is more contiguous and correct for a given level of sequence coverage.
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