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southern cattle tick
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).
|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-2015||Jun 7th, 2017|
|Rhipicephalus microplus genome assembly ASM1333972v1 (GCF_013339725.1)||Canu, FALCON, WTDBG, Smartdenovo, Quickmerge||Jun 16th, 2020|
|Functional annotation of NCBI Rhipicephalus microplus Annotation Release 100||AgBase functional annotation pipeline||Oct 8th, 2021|
|NCBI Rhipicephalus microplus Annotation Release 100||NCBI Eukaryotic Genome Annotation Pipeline||Nov 10th, 2020|