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JCVI_ISG_i3_1.0

Organism name:
Ixodes scapularis (black-legged tick)
Infraspecific name:
Strain: Wikel colony
BioSample:
SAMN03004382
BioProject:
PRJNA16232
Submitter:
Ixodes scapularis Genome Project
Date:
2008/04/18
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000208615.1 (latest)
RefSeq assembly accession:
GCF_000208615.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ABJB01
Assembly method:
unknown v. before 2008
Genome coverage:
6x
Sequencing technology:
Sanger

IDs: 276608 [UID] 270978 [GenBank] 276608 [RefSeq]

See Genome Information for Ixodes scapularis

There are 2 assemblies for this organism

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History (Show revision history)

Comment


This Wikel tick colony was established in 1996 using field collected ticks from New York, Oklahoma and a Lyme Disease endemic area of Connecticut. This colony has been continuously in-bred since establishment and has not been supplemented with field ... collected material. The colony is known to be a competent vector of various Borrelia and Babesia isolates. Genomic DNA was prepared from embryonated eggs.

The genome of Ixodes scapularis Wikel strain has been sequenced to approximately 6x coverage in a joint effort by the Broad Institute and The J. Craig Venter Institute (JCVI) and funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health. Assembly was performed at JCVI and consists of 369,492 scaffolds built from 570,637 contigs with an estimated 3.8x coverage of the assembly. The other 570958 contigs in the 01 version of this project represent degenerate contigs that were not incorporated into scaffolds. The first public assembly is deposited as JCVI_ISG_i3_1.0 and has the VectorBase Designation IscaW1. Additional information about the Ixodes scapularis sequencing project and assembly can be found at http://iscapularis.vectorbase.org/ and http://msc.jcvi.org/i_scapularis/.
The annotation for this assembly was produced in a joint effort between JCVI and VectorBase with support from The Broad Institute of Harvard/MIT. A total of 18,385 scaffolds were annotated, containing 20,486 protein coding genes, and 4,439 non-coding RNA genes. Computational annotation methods were optimized with respect to training data sets resulting in a high confidence set of predicted gene models making extensive use of protein and/or EST supporting evidence. Long-term curation of the sequence and subsequent annotation updates will be the responsibility of VectorBase at http://www.vectorbase.org.
Assembly name: JCVI_ISG_i3_1.0
Genome coverage: 3.8x on assembled contigs; 6x based on an estimated genome size of 2.1 Gbp.
Annotation was added to the scaffolds in December 2008.  more

Global statistics

Total sequence length1,765,382,190
Total assembly gap length376,910,010
Gaps between scaffolds0
Number of scaffolds369,492
Scaffold N5076,228
Scaffold L503,623
Number of contigs570,637
Contig N502,942
Contig L5088,833
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)570,637

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PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced1,765,382,190369,4921,388,472,18076,228201,1450
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