Ixodes scapularis (IscaW1)

Ixodes scapularis Assembly and Gene Annotation

The Ixodes scapularis data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and VectorBase, a component of VEuPathDB.

Picture credit (public domain): Scott Bauer (USDA) 1998

About Ixodes scapularis

Ixodes scapularis, the black-legged tick, is a hard-bodied tick from the Ixodidae family. I. scapularis is the primary vector for Lyme disease, transmitting the pathogenic bacterium Borrelia burgdorfei.

Wikkel strain

The Ixodes scapularis Wikel colony was established by Dr. S. Wikel (University of Connecticut Health Center) in 1996 using approximately 30 pairs of field collected adult male and female ticks from New York, Oklahoma and a Lyme disease endemic area of Connecticut. The colony has been continuously in-bred for approximatley twelve generations since establishment and has not been supplemented with field collected material. The colony is known to be a competent vector of various Borrelia burgdorferi (strains B31 and 297) and Babesia microti isolates. Dr. D. Sonenshine at Old Dominion University also maintains a satellite colony of the Wikel strain.

Source: VectorBase

Picture credit (public domain): Scott Bauer (USDA) 1998


The Ixodes scapularis Wikel strain genome sequence is a joint effort between the Broad Institute and the J. Craig Venter Institute (JCVI). Assembly of the estimated 4x shotgun coverage was performed at the JCVI. The assembly presented here (IscaW1, 2008) consists of 369,492 supercontigs, totalling 1,76 Gigabases, with a supercontig N50 size of 72 Kb.


The annotation of the Ixodes genome is a collaboration between VectorBase and JCVI with support from the Broad Institute. Each group generated a set of gene predictions which were merged into a single canonical set (IscaW1.1). The gene set currenty shown (IscaW1.7, July 2019) is an improvement of the initial set, with the addition of community annotation and non-coding RNA genes from the Ensembl Genomes pipeline.


  1. The Ixodes scapularis Genome Project: an opportunity for advancing tick research.
    Hill CA, Wikel SK. 2005. Trends Parasitol.. 21(4):151.
  2. Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
    Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K et al. 2016. Nat Commun.. 7
  3. Tick genomics: the Ixodes genome project and beyond.
    Pagel Van Zee J, Geraci NS, Guerrero FD, Wikel SK, Stuart JJ, Nene VM, Hill CA. 2007. International Journal for Parasitology. 37:1297-1305.



AssemblyIscaW1, INSDC Assembly GCA_000208615.1, Aug 2007
Database version108.1
Golden Path Length1,765,382,190
Genebuild byVEuPathDB
Genebuild methodImport
Data sourceVectorBase

Gene counts

Coding genes20,488
Non coding genes2,854
Small non coding genes2,853
Long non coding genes1
Gene transcripts23,342


Short Variants1,776,352