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ARS Home » Plains Area » Kerrville, Texas » Knipling-Bushland U.S. Livestock Insects Research Laboratory » LAPRU » Research » Publications at this Location » Publication #333833

Research Project: Genomics of Livestock Pests

Location: Livestock Arthropod Pests Research

Title: Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: Assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome

Author
item BARRERO, ROBERTO - Murdoch University
item Guerrero, Felicito
item BLACK, MICHAEL - Murdoch University
item MCCOOKE, JOHN - Murdoch University
item SCHILKEY, FAYE - National Center For Genome Resources
item Perez De Leon, Adalberto - Beto
item Miller, Robert
item BRUNS, SARA - Amplicon Express
item DOBRY, JASON - Amplicon Express
item MIKHAYLENKO, GALINA - Amplicon Express
item STORMO, KEITH - Amplicon Express
item BELL, CALLUM - National Center For Genome Resources
item TAO, QUANZHOU - Amplicon Express
item BOGDEN, ROBERT - Amplicon Express
item MOOLHUIJZEN, PAULA - Curtin University
item HUNTER, ADAM - Murdoch University
item BELLGARD, MATTHEW - Murdoch University

Submitted to: International Journal for Parasitology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2017
Publication Date: 8/1/2017
Citation: Barrero, R., Guerrero, F., Black, M., McCooke, J., Schilkey, F., Perez De Leon, A.A., Miller, R., Bruns, S., Dobry, J., Mikhaylenko, G., Stormo, K., Bell, C., Tao, Q., Bogden, R., Moolhuijzen, P., Hunter, A., Bellgard, M. 2017. Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: Assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome. International Journal for Parasitology. 47(9):569-583.

Interpretive Summary: The southern cattle fever tick, R. microplus, is an ectoparasite of livestock with widespread distribution in tropical and semitropical countries of the world. This tick’s genome is big and complex, with its size estimated to be 7.1 Gbp, which is approximately 2.5 times larger than the human genome. Genomes of this nature require specialized computational approaches to sequence and assemble. We report the first assembly of a tick genome that utilized hybrid sequencing and assembly approaches to capture the gene-coding regions, and the difficult to sequence repetitive fractions of this enormous genome. Our hybrid approach utilized second and third generation DNA sequencing protocols and bioinformatic computational software customized for this genome assembly project.

Technical Abstract: The genome of the cattle tick R. microplus, an ectoparasite with global distribution, is estimated to be 7.1 Gbp and consists of ~70% repetitive DNA. We report the first assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0 Gbp represented in 195,170 scaffolds with a N50 of 60,284 bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, SINEs and LTRs. We discovered 30,301 and 214 protein coding and RNA gene loci, respectively. Among the RNA genes, we identified 191 microRNA loci, with 168 having similarity to known miRNAs and 23 representing novel miRNA families.