PT  - JOURNAL ARTICLE
AU  - Jason R Miller
AU  - Sergey Koren
AU  - Kari A Dilley
AU  - Vinita Puri
AU  - David M Brown
AU  - Derek M Harkins
AU  - Françoise Thibaud-Nissen
AU  - Benjamin Rosen
AU  - Xiao-Guang Chen
AU  - Zhijian Tu
AU  - Igor V Sharakhov
AU  - Maria V Sharakhova
AU  - Robert Sebra
AU  - Timothy B Stockwell
AU  - Nicholas H Bergman
AU  - Granger G Sutton
AU  - Adam M Phillippy
AU  - Peter M Piermarini
AU  - Reed S Shabman
TI  - Analysis of the <em>Aedes albopictus</em> C6/36 genome provides insight into cell line adaptations to <em>in vitro</em> viral propagation
AID  - 10.1101/157081
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 157081
4099  - http://biorxiv.org/content/early/2017/06/30/157081.short
4100  - http://biorxiv.org/content/early/2017/06/30/157081.full
AB  - Background The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.Results The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads.Conclusions The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.