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United States Department of Agriculture

Agricultural Research Service

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Research Project: Protozoan Diseases of Livestock: Application of Genomics to Vaccine Development

Location: Animal Diseases Research

Project Number: 2090-32000-034-08
Project Type: Specific Cooperative Agreement

Start Date: Jan 01, 2014
End Date: Sep 30, 2015

Objective:
To engage in collaborative research focused on the application of genomics toward development of vaccines to protect livestock from tick borne pathogens with emphasis on East Coast Fever caused by Theileria parva. T. parva is one of several parasites that cause severe economic losses in livestock worldwide. Although these parasites continue to impact global food security safe and efficacious vaccines have been elusive. The objective of this cooperative agreement is to apply state of the art comparative and structural genomic analysis to characterize parasite genomic properties that impact vaccinology applications and define putative parasite antigens that have characteristics associated with the induction of protective immune responses.

Approach:
Comparative and structural genomic analysis will be performed by a combination of (1) Genome and transcriptome sequencing through creation of libraries (Illumina paired end and mate pair; PacBio >8 Kb strand-specific RNAseq and sequencing (1 MiSeq Illumina run; 10 PacBio SMRT cells, ¼ Hi Seq channel); (2) Analysis through genome-guided transcriptome assembly, using Trinity; and (3) targeted analysis using comparative genomics and homologs to EF-1a and Tubulin alpha chain genes. Specifically for T. parva, (1) develop a host:parasite quantification assay with qPCR; (2) structural re-annotation of the genome using Trinity and generation of gene training set for ab initio gene finders; (3) perform training and running of serveral gene finders; (4) compile cross species evidence from other apicomplexan species; and (5) generation of new gene structures using a variety of combiners such as evidence Modeler and Glean.

Last Modified: 11/20/2014
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