The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus

Abstract

BackgroundThe new genomic technologies have provided novel insights into the genetics of interactions between vectors, viruses and hosts, which are leading to advances in the control of arboviruses of medical importance. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important genus of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to provide the first reference genome for these vectors. In this study, we also report the use of the reference genome to perform initial transcriptomic analyses of vector competence for BTV.ResultsOur analyses reveal that the genome is 189 Mb, assembled in 7974 scaffolds. Its annotation using the transcriptomic data generated in this study and in a previous study has identified 15,612 genes. Gene expression analyses of C. sonorensis females infected with BTV performed in this study revealed 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2), were confirmed in this study.ConclusionsThe reference genome of C. sonorensis has enabled preliminary analyses of the gene expression profiles of vector competent and refractory individuals. The genome and transcriptomes generated in this study provide suitable tools for future research on arbovirus transmission. These provide a valuable resource for these vector lineage, which diverged from other major Dipteran vector families over 200 million years ago. The genome will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae), and together with the transcriptomic data can yield potential targets for transgenic modification in vector control and functional studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5014-1) contains supplementary material, which is available to authorized users.

Transfection of Culicoides sonorensis biting midge cell lines with Wolbachia pipientis

“…Unfortunately, knowledge of immune pathways in C. sonorensis is limited, but several immune genes have been identified and characterized in a previous study [64]. Furthermore, the availability of the C. sonorensis annotated genome (GenBank: GCA_900258525) allowed for the identification of genes in Toll, JAK/STAT and IMD pathways [65]. The upregulation of Dorsal, Cactus, STAT, PIAS, Caspar, RELISH, Attacin, and an Attacin-like anti-microbial peptides suggest that Wolbachia can affect the C. sonorensis immune system pathways in different cascades.…”

“…Perhaps, this priming of the immune system could have an effect on orbivirus proliferation in its Culicoides host. Previous transcriptome studies have demonstrated 165 genes, including genes in the Toll and IMD pathways and AMPs that were differentially expressed between vector competent or refractory C. sonorensis when challenged with a BTV infection [65]. Future studies could include the inoculation of W8- w and W3- w cell lines with the orbiviruses BTV, AHSV, SBV, and/or EHDV and determining whether a novel Wolbachia infection can induce virus inhibitory effect in C. sonorensis cells.…”

Transcriptome analysis of responses to bluetongue virus infection in Aedes albopictus cells

“…With antiviral response in mind, we focused on transcriptome changes during the early stage of infection (24 hpi), which avoided RNA degradation and interference with cell maintenance at the late stage of infection in order to guarantee the quality of cDNA libraries for transcriptome sequencing. While our manuscript was in preparation, the genome of Culicoides sonorensis, a vector of BTV, was sequenced, which will facilitate the identification of potential antiviral factors and unravel the transmission mechanism of BTV as well as other arboviruses [43]. Soon, we will investigate the alterations in the transcriptome of Culicoides sonorensis (KC) cells infected with BTV to see how the changes induced by BTV infection of KC cells differ from those in A. albopictus cells.…”

Next-generation tools to control biting midge populations and reduce pathogen transmission

“…Such sites could be re-used using targeted recombinases [ 79 ] or CRISPR-Cas9 [ 80 ]. Research suggests that BTV vector competence is associated with the expression of glutathione S transferase (GST) and the antiviral helicase (SKi2) [ 28 , 81 ]; thus, altering the expression of the two genes encoding these proteins with inserted promotors or suppressors may be a first step towards a genetically-based control strategy.…”