P1009 Sheep reference genome sequence updates: Texel improvements and Rambouillet progress

作者：Y. Liu, Shwetha C. Murali, R. Alan Harris, Adam C. English, Xiang Qin, Evette Skinner, Stephen Richards, Jason H. Rogers, Yi Han, Vanesa Vee, M. Wang, Qingchang Meng, Michael P. Heaton, Timothy P. L. Smith, Brian P. Dalrymple, James Kijas, N. E. Cockett, Eric Boerwinkle, Donna M. Muzny, Richard A. Gibbs, Kim C. Worley · 发表于：Journal of Animal Science · 年份：2016 · DOI：10.2527/jas2016.94supplement418b · 被引用次数：10 · 研究领域：Genetic and phenotypic traits in livestock、Cancer-related molecular mechanisms research

The quality of draft genome assemblies is improving beyond that of early Sanger sequencing as a result of the latest methods for producing and analyzing long reads. We have applied these methods to improve the existing genome of the Texel sheep and are in the process of producing a de novo assembly from a single Rambouillet ewe. The Texel ram Pacific Biosciences data were used with the PBJelly software1 to produce an improved assembly, Oar_v4.0 (GCA_000298735.2). This new assembly, available in GenBank, has improved contiguity with a contig N50 of 150kb and genomic representation with about 2% more genes represented in the RefSeq annotation. This highly contiguous genome has increased the contig N50 more than threefold (from 40 kb), reduced the number of gaps and contigs by two-thirds, and merged 232 scaffolds (4%). Further efforts to produce a very high quality reference genome have shifted focus to the Rambouillet breed where all of the genomic data are being collected from a single ewe. We have completed production of 200 Gb of sequence using the Pacific Biosciences technology. The data have a subread length of 12.6 kb N50 length and 8.9 kb mean length. Error correction of the reads, followed by assembly using Falcon, produced an assembly with a contig N50 of 3.6 Mb with a total length of 2.65 Gb. Two hundred twenty-seven contigs contain 50% of the sequence. Further efforts to scaffold the genome using Hi-C data are planned. Sample collection from the Rambouillet donor ani...