Ixodes scapularis (Black-legged tick, ISE6) Assembly and Gene Annotation

Picture credit (public domain): Scott Bauer (USDA) 1998

About Ixodes scapularis

Ixodes scapularis, the black-legged tick, is a hard-bodied tick from the Ixodidae family. I. scapularis is the primary vector for Lyme disease, transmitting the pathogenic bacterium Borrelia burgdorfei.

ISE6 cell line

The ISE6 cell line (Ixodes scapularis embryonic 6) is an extensively used tick cell line that has been successfully used to culture many tick-associated bacteria (Rickettsia, Anaplasma, Ehrlichia, and Neoehrlichia), to study vector-pathogen interactions and differential expression of pathogen genes during growth in mammalian and arthropod cells, to carry out growth and propagation of Arboviruses, and are an important model for molecular study using RNAi of tick genes important for decreasing pathogen transmission and understanding tick biology ( "An Ixodes scapularis cell line with a predominantly neuron-like phenotype", Oliver et al, Exp Appl Acarol. 2015 Jul; 66(3): 427--442. doi: 10.1007/s10493-015-9908-1).

Source: VectorBase

Picture credit (public domain): Scott Bauer (USDA) 1998

IscaI1 assembly

IscaI1 is a phased diploid assembly from the Ixodes scapularis ISE6 cell line, as described in 'A draft genome sequence for the Ixodes scapularis cell line, ISE6', Miller et al, F1000Res. 2018 Mar 8;7:297. doi: 10.12688/f1000research.13635.1. PacBio sequencing yielded 192.5 Gbp in 27.3 million unpaired reads, providing approximately 92X coverage of the estimated 2.1 Gbp tick genome. To overcome high base call error observed in single-molecule long-read data, the long reads were subjected to the Canu correction process which filtered, trimmed, and polished reads based on alignment with other long reads. Correction yielded 36.7 Gbp in 2.1 million reads with a 17,680 bp N50.

The corrected long reads were assembled in isolation with the Canu long-read assembler and the initial assembly, named Ise6_asm0, contained 18,717 contigs. The uncorrected long reads were used to polish the contig consensus sequences using the Arrow process. This was run in two iterations to produce assemblies Ise6_asm1 and Ise6_asm2 respectively. The released assembly, named Ise6_asm2, contained 2,691,078,110 bases in 18,717 contigs with a 269,660 bp contig N50.

IscaI1.0 gene set

Gene set IscaW1.6 projected from IscaW1 assembly, and RNA genes analysis performed.

References

1. A draft genome sequence for the Ixodes scapularis cell line, ISE6.
   Miller JR, Koren S, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG.. 2018. F1000Res.. 7
2. An Ixodes scapularis cell line with a predominantly neuron-like phenotype.
   Oliver JD, Chvez AS, Felsheim RF, Kurtti TJ, Munderloh UG. 2015. Exp Appl Acarol.. 66(3)

Picture credit: Scott Bauer (USDA) 1998