Cate Hill, Purdue Entomology, Plays an Integral Part in Release of the Lyme Disease Tick Genome Annotation

December 3, 2008
Press Release

Photo courtesy of VectorBase

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.

The genome annotation release 1.0 is now available in GenBank (accession ID ABJB010000000) and at VectorBase (non-government link).

Scientific Community Involvement

VectorBase is maintaining and will be updating the Ixodes genome annotation. The scientific community is encouraged to contribute to this annotation effort by submitting gene annotations to VectorBase. Instructions for submitting annotations can be can be found at VectorBase.

An Ixodes listserv (non-government link) 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.

Assembly Statistics

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: 369,492
Total length of combined contigs 1.4 Gbp
Total length of combined scaffolds (including gaps) 1.8 Gbp
Estimated genome size 2.1 Gbp

Annotation Release 1.0 Statistics
Transcription units-genes

Total number of genes 20,486
Mean gene length (bp) 10,589
Median gene length (bp) 4,259
Shortest gene (bp) 95
Longest gene (bp) 242,297
Total number of exons 89,663
Number of mono-exonic genes 5,707
Total number of Introns 69,163
Percentage of genes with introns 72.10%
Intergenic regions GC content 32%
Coding regions GC content 56%

Coding sequences (CDS)

Mean CDS length (bp) 855
Median CDS length (bp) 594
Shortest CDS (bp) 95
Longest CDS (bp)15,248

Supplementary Data

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.