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What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Lynsey K. Whitacre, Polyana C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, Leeson J. Alexander, View ORCID ProfileJuan F. Medrano, View ORCID ProfileRobert D. Schnabel, View ORCID ProfileJeremy F. Taylor, View ORCID ProfileJared E. Decker
doi: https://doi.org/10.1101/022731
Lynsey K. Whitacre
1Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
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Polyana C. Tizioto
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
3Embrapa Southeast Livestock, São Carlos, São Paulo 13560-970, Brazil
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JaeWoo Kim
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
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Tad S. Sonstegard
4Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
5Recombinetics Inc., 1246 University Ave W #301, St Paul, MN 55104, USA
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Steven G. Schroeder
4Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
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Leeson J. Alexander
6USDA-ARS (retired), LARRL, Fort Keogh Miles City, Montana 59301, USA
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Juan F. Medrano
7Department of Animal Science, University of California-Davis, Davis, California 95616, USA
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Robert D. Schnabel
1Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
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Jeremy F. Taylor
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
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Jared E. Decker
1Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
2Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
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  • ORCID record for Jared E. Decker
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Abstract

Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped. We generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species. We demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of infectious or symbiotic organisms.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 17, 2015.
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What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
Lynsey K. Whitacre, Polyana C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, Leeson J. Alexander, Juan F. Medrano, Robert D. Schnabel, Jeremy F. Taylor, Jared E. Decker
bioRxiv 022731; doi: https://doi.org/10.1101/022731
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What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
Lynsey K. Whitacre, Polyana C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, Leeson J. Alexander, Juan F. Medrano, Robert D. Schnabel, Jeremy F. Taylor, Jared E. Decker
bioRxiv 022731; doi: https://doi.org/10.1101/022731

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