A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes

SIMPLE SUMMARY: Mosquitoes from the family Culicidae are vectors of numerous human diseases such as dengue, Zika, and West Nile fevers, malaria, and lymphatic filariasis. The availability of high-quality genome assemblies for mosquitoes assists in identifying genes responsible for important epidemiological traits such as vector competence, insecticide resistance, and mosquito behavior and stimulates a better understanding of the genetic structure of mosquito populations. Thus, the development of genomic resources and tools is a necessary step for designing and implementing novel genome-based approaches to control mosquitoes. The emphasis of this study is the further development and optimization of a physical genome mapping approach. Physical mapping is placing genomic scaffolds to the chromosomes based on hybridization of the specific probes. This task is difficult for mosquitoes with large genome sizes which are enriched with repetitive DNA sequences and can be potentially misassembled. Here, we describe in detail a simple and robust technique for the physical mapping of such mosquito genomes. This method can be further used for physical genome mapping in other mosquitoes and insects. ABSTRACT: Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemblies for mosquitoes with repeat-rich genomes, which can potentially be misassembled. In this study, we describe a new gene-based physical mapping approach that was optimized using the newly assembled Aedes albopictus genome, which is enriched with transposable elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene transcripts were used for the probe design. Instead of using genomic DNA, complementary DNA was utilized as a template for development of the PCR-amplified probes for FISH. All probes were successfully amplified and mapped to specific chromosome bands. The genome-unique probes allowed to perform unambiguous mapping of genomic scaffolds to chromosome regions. The method described in detail here can be used for physical genome mapping in other insects.