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The 454 data was from a Texel ram collected by Tim Smith of (US Meat Animal Research Center (USMARC)) at the Clay Center in Nebraska, USA. Sex: male, Breed : Texel, Isolate number: 200118011, Country of Origin: USA, Isolation ... Source: Blood, Collection Date: Late 2009. Most of the Illumina data was from a 6-month old ewe collected by Dr. Jacob B. Hansen of the University of Copenhagen. Sex: female, Breed: Texel, Isolate number: N/A, Country of Origin: Denmark, Isolation Source: Blood, Collection Date: Late 2009.

A single Texel ewe and a single Texel ram were sequenced and the 75-fold coverage by Illumina reads of the Texel ewe were assembled de novo into contigs and scaffolds with SOAPdenovo. Then 120-fold coverage Illumina sequences from both the ewe and the ram were used for a round of gap-filling. At this point, the N50 length of contigs was 18 kb, and the N50 length of the assembled scaffolds was 1.1Mb, achieving a total length of 2.64 Gb and leaving 6.9% gaps. This assembly was the previous Oar v2.0. The current assembly, Oar_v3.1, was created with another round of gap-filling by adding 21-fold coverage of GC content unbiased Illumina sequencing data from the male and 3 Gb MeDIP-seq for high GC content sequence from the female to the original datasets. Approximately 200,000 gaps were filled, including about 5000 that were filled using CHORI-243 BAC library sequences and 454 reads generated for the Oar v1.0 assembly (ACIV000000000, BioProject PRJNA33937). Segmental duplicates were identified by Whole Genome Assembly Comparison (WAGC), and their read coverage checked by GC content adjustment. Probable artificial tandem duplicates were identified using the larger insert 454 and BAC libraries and comparison to the UMD3 bovine genome assembly, and one copy of the tandem pairs was removed. The assembly of 775 overlapping scaffold ends were revised and these adjacent scaffold pairs were linked together. Artificial duplicated copies that had been generated by multiple gap-filling steps using gapcloser were removed, and erroneously assembled scaffolds identified during the error checking were manually split. A high-density RH map with 39,042 SNP markers and Ovine SNP50 genotyping linkage data were used to check scaffold integrity and to anchor scaffolds and super-scaffolds to chromosomes, leaving roughly 5700 unplaced scaffolds.
For more information about the International Sheep Genomics Consortium (ISGC) and the sheep assembly, see http://www.sheephapmap.org/  more

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