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Rhipicephalus microplus

Summary
Resource Type
Organism
Genus
Rhipicephalus
Species
microplus
Common Name
southern cattle tick
Description

The Metastriata line of hard ticks consists of 13 genera and over 459 species, including many species of medical and veterinary importance across the genera Rhipicephalus, Hyalomma, Hemaphysalis, Amblyomma, and Dermacentor. Rhipicephalus (Boophilus) microplus, the southern cattle tick, is a livestock ectoparasite that is a vector for the pathogenic organisms causing bovine babesiosis and anaplasmosis. Annual economic losses attributable to R. microplus infestations have been recently estimated in Brazil alone to be approximately $2 billion.  

R. microplus was a serious cattle pest in the U. S. in the early 1900s, with estimated annual losses to the U. S. cattle industry of $3 billion in today's dollars. An aggressive control program led to the eradication of the tick from the U. S. However, ecological and climactic factors have emerged that threaten the eradication status of the U.S. with regards to R. microplus. This drove the initiation of a cattle tick genome sequencing project in 2005, focusing upon acquisition of ESTs and gene-rich regions of the genome, as the estimated genome size of 7.1 Gbp and the highly repetitive nature precluded whole genome sequencing at that time. Eventual maturation of long-read sequencing technologies enabled a hybrid Pac Bio-Illumina sequencing/assembly approach for the project. Assembly Rmi_v2.0 used long reads of very high molecular weight genomic DNA by PacBio protocols. A subset of these reads was error-corrected by an assembled set of Illumina-generated contigs sourced from genomic DNA purified by reassociation kinetics protocols selecting for the unique low-copy genome fraction. Assembly Rmi_v2.0 was generated by an international effort led by Dr. Felix D. Guerrero (USDA-ARS Knipling-Bushland U. S. Livestock Insects Research Laboratory, Kerrville, TX, USA) with fellow project consortium leaders Dr. Matthew I. Bellgard (Centre for Comparative Genomics, Murdoch University, Murdoch, Australia) and Dr. Robert J. Miller (USDA-ARS Cattle Fever Tick Research Laboratory, Edinburg, TX, USA) through funds provided by USDA-ARS.

Genome update: The i5k Workspace@NAL previously hosted assembly Rmi_v2.0 (https://i5k.nal.usda.gov/bio_data/836696). This assembly has been updated to assembly ASM1333972v1 (GCF_013339725.1; https://i5k.nal.usda.gov/bio_data/1141198) and annotations NCBI Rhipicephalus microplus Annotation Release 100 (https://i5k.nal.usda.gov/bio_data/1141200).

Publication
  1. Guerrero FD, Moolhuijzen P, Peterson DG, Bidwell S, Caler E, Bellgard M, Nene VM, Djikeng A. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus.. BMC genomics. 2010 Jun 11; 11:374.
  2. McCooke JK, Guerrero FD, Barrero RA, Black M, Hunter A, Bell C, Schilkey F, Miller RJ, Bellgard MI. The mitochondrial genome of a Texas outbreak strain of the cattle tick, Rhipicephalus (Boophilus) microplus, derived from whole genome sequencing Pacific Biosciences and Illumina reads.. Gene. 2015 Oct 15; 571(1):135-41.
  3. Barrero RA, Guerrero FD, Black M, McCooke J, Chapman B, Schilkey F, Pérez de León AA, Miller RJ, Bruns S, Dobry J, Mikhaylenko G, Stormo K, Bell C, Tao Q, Bogden R, Moolhuijzen PM, Hunter A, Bellgard MI. 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. 2017 08; 47(9):569-583.
  4. Jia N, Wang J, Shi W, Du L, Sun Y, Zhan W, Jiang JF, Wang Q, Zhang B, Ji P, Bell-Sakyi L, Cui XM, Yuan TT, Jiang BG, Yang WF, Lam TT, Chang QC, Ding SJ, Wang XJ, Zhu JG, Ruan XD, Zhao L, Wei JT, Ye RZ, Que TC, Du CH, Zhou YH, Cheng JX, Dai PF, Guo WB, Han XH, Huang EJ, Li LF, Wei W, Gao YC, Liu JZ, Shao HZ, Wang X, Wang CC, Yang TC, Huo QB, Li W, Chen HY, Chen SE, Zhou LG, Ni XB, Tian JH, Sheng Y, Liu T, Pan YS, Xia LY, Li J, Tick Genome and Microbiome Consortium (TIGMIC), Zhao F, Cao WC. Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.. Cell. 2020 09 03; 182(5):1328-1340.e13.
Organism Image
Image Credit
Two Rhipicephalus microplus replete females by Jason Tidwell, license: CC-BY-SA 4.0
Analysis
NameProgramDate Constructed
Rhipicephalus microplus genome assembly Rmi v2.0 (GCA_002176555.1)SOAPdenovo v. MAY-2015; Ray v. MAY-2015; Cap3 v. JUNE-2015; PBJelly v. NOVEMBER-2015; CANU v. DECEMBER-2015Jun 7th, 2017
Rhipicephalus microplus genome assembly ASM1333972v1 (GCF_013339725.1)Canu, FALCON, WTDBG, Smartdenovo, QuickmergeJun 16th, 2020
Functional annotation of NCBI Rhipicephalus microplus Annotation Release 100AgBase functional annotation pipelineOct 8th, 2021
NCBI Rhipicephalus microplus Annotation Release 100NCBI Eukaryotic Genome Annotation PipelineNov 10th, 2020
Assembly Stats
Contig N50
NA
Scaffold N50
183,350,851
GC Content
46.11
Other Information
Community Contact
Perot Saelao|perot.saelao@usda.gov
Links