Genome-Plasticity-Informed Quality Improvements to Interpretation of Anopheles Cell Line Proteomics

INTRODUCTION: Molecular biology approaches remain underutilized in mosquito research. Mosquitoes exhibit high genome plasticity and incomplete speciation, both of which should contribute to genomic sequencing interpretation and the resulting proteomes. New approaches are needed for the prevention of mosquito-borne diseases in the face of mounting resistance to drugs and pesticides. We seek to leverage analysis of genome variation for a better understanding of the mosquito proteome, 40% of which is functionally uncharacterized, as a target pool for interventions.

METHODS: Sample data were obtained from the NIH NCBI Sequence Read Archive (SRA). Our approach was designed with a previous study in Aedes aegypti (PMID: 28103802) by others in mind to ensure optimal benefits from comparative analysis. Analyses were performed in Galaxy. The Integrated Genome Browser (IGB) and Microsoft Office products were used to visualize and quantify results.

RESULTS: Analysis of available Anopheles cell-line-derived genomes identified meaningful differences between lines that can improve proteomics analysis. Using browser windows, we showcase novel indel edits that represent improvements to gene models present in the current WT consensus. We describe the possible variations’ effects on protein structure in aggregate and for specific examples relevant to the current literature.

CONCLUSION/DISCUSSION: Genomics-informed proteomics will continue to benefit from additional information about the expected level of variation expected within, or between, samples. With this information in mind, we can seek to apply our approach to additional cell lines in order to better understand and identify the best targets for transmission intervention approaches to limit mosquito-borne diseases.