A draft genome sequence for the Ixodes scapularis cell line, ISE6

Jason R Miller; Sergey Koren; Kari A Dilley; Derek M Harkins; Timothy B Stockwell; Reed S Shabman; Granger G Sutton

doi:10.12688/f1000research.13635.1

A draft genome sequence for the Ixodes scapularis cell line, ISE6

F1000Res. 2018 Mar 8:7:297. doi: 10.12688/f1000research.13635.1. eCollection 2018.

Authors

Jason R Miller^{1

2}, Sergey Koren³, Kari A Dilley¹, Derek M Harkins¹, Timothy B Stockwell^{1

4}, Reed S Shabman^{1

5}, Granger G Sutton¹

Affiliations

¹ J. Craig Venter Institute, Rockville, MD, 20850, USA.
² Shepherd University, Shepherdstown, WV, 25443, USA.
³ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA.
⁴ NBACC, Fort Detrick, MD, 21702, USA.
⁵ ATCC, Gaithersburg, MD, 20877, USA.

Abstract

Background: The tick cell line ISE6, derived from Ixodes scapularis, is commonly used for amplification and detection of arboviruses in environmental or clinical samples. Methods: To assist with sequence-based assays, we sequenced the ISE6 genome with single-molecule, long-read technology. Results: The draft assembly appears near complete based on gene content analysis, though it appears to lack some instances of repeats in this highly repetitive genome. The assembly appears to have separated the haplotypes at many loci. DNA short read pairs, used for validation only, mapped to the cell line assembly at a higher rate than they mapped to the Ixodes scapularis reference genome sequence. Conclusions: The assembly could be useful for filtering host genome sequence from sequence data obtained from cells infected with pathogens.

Keywords: ISE6; Ixodes scapularis; cell line; genome; tick.

Grants and funding

JCVI staff was supported by DHS contract HSHQDC-15-C-B0059. SK was supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.