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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #289052
Title: Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads

Author
item Schroeder, Steven - Steve
item ZIMIN, ALEKSEY - University Of Maryland
item Bickhart, Derek
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item GARCIA, FERNANDO - Universidade Estadual Paulista (UNESP)

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/21/2012
Publication Date: 1/14/2013
Citation: Schroeder, S.G., Zimin, A., Bickhart, D.M., Sonstegard, T.S., Van Tassell, C.P., Garcia, F.J. 2013. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads. Poster P0523, pp.237.

Interpretive Summary:

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.