Location: Cattle Fever Tick Research UnitTitle: Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus
|GHAFFARI, NOUSHIN - Prairie View A & M University
|METZ, RICHARD - Texas A&M Agrilife
|DICKENS, CHARLES - Texas A&M University
|BLOOD, PHILIP - Carnegie Mellon University
|Perez De Leon, Adalberto - Beto
|TEEL, PETE - Texas A&M University
|JOHNSON, CHARLES - Texas A&M Agrilife
Submitted to: Data in Brief
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2021
Publication Date: 2/6/2021
Publication URL: https://handle.nal.usda.gov/10113/7267162
Citation: Guerrero, F., Ghaffari, N., Bendele, K.G., Metz, R.P., Dickens, C.M., Blood, P.D., Tidwell, J.P., Miller, R., Perez De Leon, A.A., Teel, P.D., Johnson, C.D. 2021. Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus. Data in Brief. 35. https://doi.org/10.1016/j.dib.2021.106852.
Interpretive Summary: This manuscript reports the sequence and assembly of two high quality genomes of the Rhipicephalus microplus and Rhipicephalus annulatus, which are important cattle parasites that are known to vector multiple bovine pathogens. The assembled genomes reported in this manuscript provide data that can be used by researchers interested in studying arachnid and tick genomics, arachnid evolution, and comparative genomics. The dataset provides information to researchers who are interested in studying genes involved in the development of pesticides resistance and to identify targets with chemical entities with acaricidal activity for anti-tick vaccine approaches.
Technical Abstract: Ticks from the genus Rhipicephalus have enormous global economic impact as ectoparasites of cattle. Rhipicephalus microplus and Rhipicephalus annulatus are known to harbour infectious pathogens such as Babesia bovis, Babesia bigemina, and Anaplasma marginale. Having reference quality genomes of these ticks would advance research to identify druggable targets for chemical entities with acaricidal activity and refine anti-tick vaccine approaches. We sequenced and assembled the genomes of R. microplus and R. annulatus, using Pacific Biosciences and HiSeq 4000 technologies. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq 4000 and the long-read PacBio Sequel platforms. We used 22 and 29 SMRT cells on the Pacific Biosciences Sequel for R. microplus and R. annulatus, respectively, and 3 lanes of the Illumina HiSeq 4000 platform for each tick. The PacBio sequence yields for R. microplus and R. annulatus were 21.0 and 27.9 million subreads, respectively, which were assembled with Canu v. 1.7 on a reserved Pittsburgh Supercomputing Center Bridges system node with access to 12 TB of RAM, each assembly running continuously for 24 and 29 days. The final Canu assemblies consisted of 92,167 and 57,796 contigs with an average contig length of 39,249 and 69,055 bp for R. microplus and R. annulatus, respectively. Annotated genome quality was assessed by BUSCO analysis to provide quantitative measures for each assembled genome. Over 82% and 92% of the 1066 member BUSCO gene set was found in the assembled genomes of R. microplus and R. annulatus, respectively. For R. microplus, only 189 of the 1066 BUSCO genes were missing and only 140 were present in a fragmented condition. For R. annulatus, only 75 of the BUSCO genes were missing and only 109 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information. The data presented here are related to the research article "Comparative genomics of the cattle ticks, Rhipicephalus microplus and Rhipicephalus annulatus, using high quality long-read assembled genomes, focusing upon genes involved in pesticide resistance".