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Sequence Set Browser

 

ABJB000000000.1 Ixodes scapularis

Master
# of Contigs: 1,141,595
# of Proteins: 20,486
# of Scaffolds/Chrs: 369,492
Total length: 1,895,741,386 bp
BioProject: PRJNA16232
BioSample: SAMN03004382
Keywords: WGS
Annotation: Scaffolds
Organism: Ixodes scapularisshow lineagehide lineage
Biosource:
/dev_stage = embryonated eggs
/mol_type = genomic genomic
/strain = Wikel colony
WGS: ABJB010000001:ABJB011141595
Scaffolds: DS611849:DS981340
369,492 scaffolds, 20,486 proteins, total length is 1,765,382,190 bases
Reference:
Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis : PLoS Genet. 11 (3), E1005120 (2015) – show 11 authorshide authors
Ayllon,N., Villar,M., Galindo,R.C., Kocan,K.M., Sima,R., Lopez,J.A., Vazquez,J., Alberdi,P., Cabezas-Cruz,A., Kopacek,P., de la Fuente,J.
Submission:
Submitted (11-DEC-2007) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA – Nene,V., Ixodes scapularis Genome Project
Submission:
Submitted (21-FEB-2008) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA – Nene,V., Ixodes scapularis Genome Project

The Ixodes scapularis whole genome shotgun (WGS) project has the project accession ABJB000000000. This version of the project (01) has the accession number ABJB010000000, and consists of sequences ABJB010000001-ABJB011141595.

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.

##Genome-Assembly-Data-START##
Assembly Method : unknown v. before 2008
Assembly Name : JCVI_ISG_i3_1.0
Genome Coverage : 6x
Sequencing Technology : Sanger
##Genome-Assembly-Data-END##
Contigs
Download
GenBank:ABJB01.1.gbff.gz 184.9 Mb
 ABJB01.2.gbff.gz 185.4 Mb
 ABJB01.3.gbff.gz 185.5 Mb
 ABJB01.4.gbff.gz 185.6 Mb
 ABJB01.5.gbff.gz 169.9 Mb
ASN.1:ABJB01.1.bbs.gz 98.4 Mb
 ABJB01.2.bbs.gz 98.6 Mb
 ABJB01.3.bbs.gz 98.7 Mb
 ABJB01.4.bbs.gz 98.7 Mb
 ABJB01.5.bbs.gz 90.4 Mb