Cytogenetic Studies of Polytene Chromosomes and Physical Genome Mapping for the Mosquito Culex quinquefasciatus Say, 1823; Transposable Element Annotation of Several Insect-Vector Species

In this thesis I collected several long-term projects which were done in a course of seven years. All of them have direct relation to the medically and veterinary important insect species which are able to transmit human and animal pathogens. I hope that this collection of material and observations can serve to the humanity and contribute towards saving lives.

The first chapter is devoted to Culex quinquefasciatus, southern house mosquito, polytene chromosomes and an investigation of the non-trivial task of obtaining polytene chromosomes for cytogenetic studies. In this chapter, I summarize certain observations about mosquito physiology and how that relates and contributes to highly-polytenized chromosomes of various mosquito tissues. A method of chromosomal preparation is described, tailored specifically to this species. Specific conditions were determined which help to raise mosquito larvae with highly polytenized tissues. Finally, a Maria F. Unger morphological characteristic of mosquito larvae is described, which helps to pinpoint a stage of development which is best for obtaining well-developed polytene chromosomes.

The second chapter of this thesis is devoted to the results based on the investigation in chapter 1. The making of a standard cytogenetic map for Culex quinquefasciatus is described, which is a base for physical mapping and finishing the Culex genome assembly, as well as a strong contribution to population genetic studies. Next, the application of the new cytogenetic map is demonstrated with the physical mapping of 16 supercontigs and 6 genetic markers. The physical map is integrated with a previously made genetic linkage map based on the physical mapping results, with 13 total matches. The polytene chromosome names are set according to the genetic linkage map. Two genome misassembles are found using fluorescent in situ hybridization.

The third and final chapter is devoted to the genome annotation of transposable elements. The semi-automated pipeline is developed and tested on several insect-vector species. The evolution of this pipeline is demonstrated with its implementation on Pediculus humanus, Culex quinquefasciatus, and Ixodes scapularis; the beginning work in two Phlebotomus genomes and several Anopheline genomes is also discussed.

In conclusion, by studying insect vectors and zooming in on their genomes, and by learning about their specific features and commonalities, we contribute to the understanding of what makes those organisms efficient vectors and how to control them and the spread of the diseases which they transmit.