Release of preliminary 0.5 gene annotation of Ixodes scapularis (ABJB010000000), April 29, 2008
The National Institute of Allergy and Infectious Diseases, National Institutes of Health has funded the sequencing, assembly and annotation of the genome of the Lyme disease tick, Ixodes scapularis, through its Microbial Sequencing Centers (the J. Craig Venter Institute (JCVI) (non-government link) and the Broad Institute (non-government link) of MIT and Harvard) and the NIAID-funded Bioinformatics Resource Center, VectorBase (non-government link), at the University of Notre Dame.
JCVI and VectorBase have each prepared preliminary gene sets. They are available for download and BLAST searching as transcript and peptide FASTA files. These are preliminary and will be replaced with a first official gene set in August, 2008 Long-term curation of the sequence and subsequent annotation updates will be the responsibility of VectorBase.
Scientific Community Involvement
Ixodes researchers are encouraged to contribute to the annotation effort by sharing their own gene models. These can be considered for incorporation into the initial gene set and can also be made public in a separate manual annotation track in future releases of the genome browser. An Ixodes list serv is hosted by Vectorbase and is moderated by Dr. Catherine Hill (Purdue University) to communicate information and announcements, and to establish a discussion forum regarding the Ixodes scapularis genome sequence and its annotation. Instructions on how to contribute to the community annotation of the genome will be communicated through the listserv.
Assembly Statistics and Supplementary Data
Total number of sequence reads: 17.4 million
Total number of sequence reads placed in the assembly: 7.3 million
Estimated fold coverage of the assembly: 3.8 fold
Number of contigs deposited in GenBank 1,141,594
Number of contigs in used in assembly: 570,637
Number of scaffolds: 369,495
Total length of combined contigs 1.4 Gbp
Total length of combined scaffolds (including gaps) 1.8 Gbp
Estimated genome size 2.1 Gbp
Complementary to the sequencing and annotation project described above, the National Institute of Allergy and Infectious Diseases, National Institutes of Health has also funded production of additional Ixodes scapularis genome-related resources. As part of this project 183,834 Ixodes scapularis EST sequences and 45 BAC sequences generated from a variety of libraries have been released in GenBank. The ESTs accession range is : EW781064-EW964897. The BAC sequence accession ranges are: AC192414-AC192429, AC192742-AC192744, AC200531, and AC205630-AC205654. More than 370,000 BAC clones have also been end sequenced and are available from the NCBI trace archive and at VectorBase.
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