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

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

Jason R Miller  1   2 , Sergey Koren  3 , Kari A Dilley  1 , Derek M Harkins  1 , Timothy B Stockwell  1   4 , Reed S Shabman  1   5 , Granger G Sutton  1
Affiliations

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

Jason R Miller et al. F1000Res. .

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.

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Conflict of interest statement

Competing interests: SK has received travel support to speak at Oxford Nanopore conferences.

Figures

Figure 1.
Figure 1.. Long read coverage of the cell line assembly.
Read coverage per base was computed by mapping uncorrected long reads to assembled contigs. Colors were added to highlight the following interpretation. Green: the minor peak of low-coverage bases suggests 87 Mbp of contig bases lies near breakpoints such as contig ends and false joins. Blue: the dominant peak, with mode at 34X, suggests that 1769 Mbp of the assembly is haplotype-separated sequence possibly representing 885 Mbp of the diploid genome. Yellow: the shoulder near 64X suggests that about 654 Mbp of the diploid genome is captured as diploid-consensus sequence. Red: high coverage (including bases not shown with coverage over 100X) suggests that under-represented genomic repeats occupy 54 Mbp of the assembly but more of the genome.
See this image and copyright information in PMC

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