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United States Department of Agriculture

Agricultural Research Service

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Research Project: Veterinary Pest Genome Sequencing and Transcriptome Analysis

Location: Tick and Biting Fly Research

Project Number: 3094-32000-036-46
Project Type: Specific Cooperative Agreement

Start Date: May 01, 2014
End Date: Apr 30, 2018

Objective:
Facilitate the assembly and annotation of the horn fly genome and transcriptome by acquisition of sequence data from the next-generation Illumina sequencing platform and the third generation Pacific Biosciences sequencing platform. Both approaches will provide new sequence information that will ensure complete coverage of the horn fly transcriptome, and provide horn fly genome sequences of sufficient length to traverse many of the anticipated problematic highly repetitive regions of the genome. Additionally, the collaborator's expertise with Illumina and Pacific Biosciences technologies will be essential and their bioinformatics staff will be critical in analysis of the data.

Approach:
1. Illumina RNA-Seq approach will be used for deep sequencing the transcriptome of the horn fly. This approach is estimated to acquire approx. 95% of the transcribed genes of the organism. Selected transcriptome analysis of dissected organs or tissues could be targeted by this approach, with the midgut a likely tissue of interest. Bioinformatic analysis will also be required to assemble and annotate this data. 2. Pacific Biosciences Third Generation sequencing technology will be used for library synthesis and SMRT cell protocol optimized for long read sequencing. Specialized bioinformatic analysis will be required for interpretation, assembly, and annotation of this dataset.

Last Modified: 10/31/2014
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