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Liu Y
,
Qin X
,
Song XZ
,
Jiang H
,
Shen Y
,
Durbin KJ
,
Lien S
,
Kent MP
,
Sodeland M
,
Ren Y
,
Zhang L
,
Sodergren E
,
Havlak P
,
Worley KC
,
Weinstock GM
,
Gibbs RA
.
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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.
Figure 1. The Genome Assembly process. Sequence from pooled BACs, individual BACs and Whole Genome Shotgun was combined in a number of different ways as outlined here. At the top left, pooled BACs were deconvoluted and assembled as individual BACs. On the top right, individually sequenced BACs were also assembled as individual BACs. Overlapping WGS data was added to all BACs and each was assembled as an enriched BAC (eBAC) using three different assembly methods. The best assembly of each eBAC was used in the merging and scaffolding steps. On the left, WGS data was assembled as a WGS assembly to produce Btau_2.0. Contigs from this assembly that were not contained within the eBACs were used to fill gaps in the BAC assembly. The sequence scaffolds were placed on chromosomes using the composite map (Integrated Bovine Map) to produce Btau_3.1. Some scaffolds were split and a multi-step placement procedure described in the text was used to place scaffolds on chromosomes for version Btau_4.0. A more complete description can be found in the text.
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