Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation

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. BACKGROUND Insect cell lines such as Aag2 and C6/36 are critical platforms for insect biology and virology. The Aedes albopictus clone C6/36 (ATCC CRL-1660) cell line is commonly used for detection, propagation, and analysis of arboviruses, including antibody-based detection of viruses in saliva [reviewed in [1]]. C6/36 cells have a short population doubling time and are . CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/157081 doi: bioRxiv preprint first posted online Jun. 30, 2017;