Ixodes Scapularis Genome Project
On December 3rd, 2008, the NIAID Microbial Sequencing Centers announced annotation Release 1.0 of the Ixodes scapularis genome sequence (GenBank accession ABJB010000000.) This annotation was produced jointly by the J. Craig Venter Institute, the VectorBase Bioinformatics Resource Center with support from the Broad Institute of Harvard/MIT.
Annotation release 1.0 was generated by comparing and merging gene sets produced independently by VectorBase and JCVI. Release 1.0 contains 20,486 high confidence protein-coding genes. VectorBase will be responsible for the long-term curation of the genome sequence and subsequent annotation updates.
Our structural annotation (gene prediction) strategy involved masking repetitive DNA sequences, followed by a combination of EST and protein alignments, trained gene prediction algorithms, and homology-based gene predictions. For functional name assignments we have used a pipeline that employed sequence similarity to PANTHER, Drosophila (Release 4.3) and UniProt-SwissProt databases.
The blacklegged or deer tick, transmits a number of organisms that cause disease, but is best known as the principal vector of Borrelia burgdorferi, the causative agent of Lyme disease. Ticks rank second to mosquitoes in importance as vectors of human disease. The goal of the sequencing project is to provide genomic resources to support research on this and related tick species.
The Ixodes scapularis genome appears to be very large in size, ~ 2.1 Gbp. The Broad Institute and The Institute for Genomic Research (TIGR), NIAID's contract Microbial Sequencing Centers, will jointly participate in this project. The MSCs will generate an assembly derived from random shotgun sequencing of the tick genome to six-fold sequence coverage. In addition, EST and BAC end sequence data and complete BAC insert sequences of some randomly selected and community defined BAC clones will be generated.