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United States Department of Agriculture

Agricultural Research Service

Research Project: MINING THE GENOME OF RHIPICEPHALUS MICROPLUS TO DEVELOP NOVEL CONTROL TECHNOLOGY AND VACCINES

Location: Tick and Biting Fly Research

Title: CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

Authors
item Bellgard, Matthew -
item Moolhuijzen, Paula -
item Guerrero, Felix
item Schibeci, David -
item Rodriguez-Valle, Manuel -
item Peterson, Daniel -
item Dowd, Scot -
item Barrero, Roberto -
item Hunter, Adam -
item Miller, Robert
item Lew-Tabor, Alae -

Submitted to: International Journal for Parasitology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 17, 2011
Publication Date: February 1, 2012
Citation: Bellgard, M.I., Moolhuijzen, P.M., Guerrero, F., Schibeci, D., Rodriguez-Valle, M., Peterson, D.G., Dowd, S.E., Barrero, R., Hunter, A., Miller, R., Lew-Tabor, A. 2012. CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus. International Journal for Parasitology. 42:161-169.

Interpretive Summary: The Rhipicephalus microplus genome is large and complex in structure, determined to be over 7.1 billion base pairs. By comparison, the human genome is approximately 3 billion base pairs. Determination of the genome sequence for the cattle will provide gene information that will facilitate the development of novel tick control technologies. To sequence the R. microplus genome, a significant amount of money would be required for the sequencing and the computational analysis necessary to assemble the sequence into a meaningful database. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome and assembling a web-based searchable dataset for researchers worldwide to access. As a significant first step, we have sequenced and assembled cattle tick genomic DNA, into a dataset that represents over 1.8 billion base pairs of DNA from gene-enriched regions of the R. microplus genome. A web-based resource was developed to enable the scientific community, to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is called CattleTickBase.

Technical Abstract: The Rhipicephalus microplus genome is large and complex in structure, making a genome sequence difficult to assemble and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gbp of DNA from gene-enriched regions of the R. microplus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genome and transcriptome sequence data at approximately 0.9x coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process, the CattleTickBase resource will continue to be updated.

Last Modified: 7/24/2014
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