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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads

Authors
item Schroeder, Steven
item Zimin, Aleksey -
item Bickhart, Derek
item Sonstegard, Tad
item Van Tassell, Curtis
item Fernando, Garcia -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: November 27, 2012
Publication Date: N/A

Technical Abstract: A de novo genome assembly of Bos taurus indicus sub-species, specifically a Nelore bull, has been developed using a multi-platform sequencing strategy. Genome sequence data for assembly (>120 Gb) was produced from Roche FLX454 and Illumina GAIIx platforms using paired-end reads from long (5 and 20 kb) and short (300 and 500 bp) insert libraries and single-end shotgun reads. After trimming for redundancy and chimeric sequences, long insert mate-pair reads yielded 175X clone (distance) coverage of the genome, while short libraries yielded 27X sequence (depth) coverage. An additional 1X and 3X sequence coverage was generated with 350 and 80 bp shotgun reads, respectively. The initial assembly is being created using the Celera assembler. A high resolution linkage map (~46,000 SNP markers) is also being developed to improve chromosome builds. Additionally, ~10X sequence coverage has been generated with PacBio long reads. This data has been applied to improving the de novo assembly in contig joining and gap closure.

Last Modified: 10/30/2014
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