Appels, R.

Barrero, R.

Bellgard, M.

Guerrero, F.D.

Hunter, A.

Lew-Tabor, A.

Moolhuijzen, P.

Rodriguez-Valle, M.

Schibeci, D.

English

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TTP7: Ticks and Tick-borne pathogens International Conference. Zaragoza (Spain), 201187A NEW WEB-BASED  GENOMICS RESOURCE  FOR BIOINFORMATICS ANALYSIS OF RHIPICEPHALUS (BOOPHILUS) MICROPLUS: CATTLETICKBASE.Corresponding Author:  Ala Lew-Tabor, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland, Brisbane, Australia. E-Mail: a.lewtabor@uq.edu.auAuthors: Bellgard, Matthew; Moolhuijzen, Paula; Guerrero, Felix; Appels, Rudi; Schibeci, David; Rodriguez Valle, Manuel; Barrero, Roberto; Hunter, Adam; Lew-Tabor, Ala KeywordsGenomics, tick, bioinformaticsIntroductionA new web-based  genomics resource for  bioinformatics  analysis of  Rhipicephalus (Boophilus) microplus: CattleTickBaseBellgard, M.I.1,2, Moolhuijzen, P.M.1,2, Guerrero, F.D.1,3, Appels, R.2, Schibeci, D.2, Rodriguez Valle, M.1,4, Barrero, R.A.2, Hunter, A.2, *Lew-Tabor, A.E.1,2,41Cooperative  Research  Centre  for  Beef  Genetic Technologies, Armidale,  NSW, Australia;  2Centre  for Comparative  Genomics,  Murdoch  University,  Perth,  Western  Australia  6150,  Australia;  3USDA-ARS Knipling  Bushland  US  Livestock  Insect  Research Laboratory, 2700  Fredericksburg  Rd.,  Kerrville,  TX 78028, USA; 4Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Qld, 4072, Australia.The Rhipicephalus (Boophilus) microplus genome is large and complex in structure (~7.1Gb consisting of over 70% repetitive DNA), 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 sequenced, assembled and annotated over 2 Gb of sequence comprised from Cot-filtered genomic DNA, ~10,000 BAC-ends, 15 targeted whole BACs  ~1.5 Mb  (Guerrero  et  al.  2010,  Bellgard,  unpublished),  ~21  Mb  from  eight  whole  transcriptome  library assemblies  representing  over  75,000  transcripts  (Wang et  al. 2007; Barrero  et al.,  unpublished)  and microRNAs (Barrero et al. 2011). The Cot-filtered genomic DNA encodes 144 Mbp of assembled contigs derived from three Cot re-association experiments that utilised methodologies  to select sequences  that are depleted in repetitive elements, from randomly sheared genomic DNA fractions, to preferentially enrich putative  gene coding regions  (Guerrero et al 2010; Bellgard  et  al. unpublished). Our  consortium has acquired genome and transcriptome sequence data at approximately 0.9x coverage of the gene-coding regions of the R. microplus genome. We also have integrated several gene expression datasets derived from selected tick  life stages  and key organs  (Rodriguez Valle et al. 2010, Barrero et al. 2011). A web-based resource was  developed to enable the tick  research scientific community to access  our datasets and conduct analysis through a single web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed ‘CattleTickBase’ and also includes access to public databases in order to undertake R. microplus sequence analysis  against all available resources  within a single integrated resource. The YABI tool at CattleTickBase will facilitate access  and manipulation of cattle tick  genome sequence data as the genome sequencing of R. microplus progresses.Acknowledgements: Beef CRC, Queensland government.

A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase

http://researchrepository.murdoch.edu.au/13074/

A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase

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