Genome annotation and evolution of chemosensory receptors in spider mites

Understanding the evolution of species and speciation, the mechanism producing the diversity of life on Earth, has always fascinated scientists. In recent years, advances in next generation sequencing techniques, together with the development of data analyzing software tools, allow us to sequence and analyze genomes of many species and reconstruct their evolutionary history. We can detect the evolutionary changes of a group of species or of different populations of a single species. In this thesis, we perform studies on three spider mite genomes, Tetranychus urticae, Tetranychus evansi and Tetranychus lintearius. The spider mites belong to the Chelicerata, the second largest group of arthropods after insects. While many insect genomes were sequenced and analyzed already, Tetranychus urticae represents the first complete chelicerate genome. This thesis has been organized into five chapters. The introductory Chapter 1 provides an overview of the explosion of genome sequences in times of the fast development of next generation sequencing techniques, describes genome annotation information, methods and pipelines to give biological meaning to these genomes, and explains the importance of genome based research for the evolution of arthropod-plant interactions. In addition, a short overview of the chemosensory receptors is provided since in the thesis we have particularly studied the annotation and evolution of this gene family in three different spider mites. Chapter 2 provides the results of annotation and analysis of the Tetranychus urticae genome (London strain). T. urticae represents one of the most polyphagous arthropod herbivores, feeding on more than 1,100 plant species including species known to produce toxic compounds. We have annotated the T. urticae genome with support of RNA-seq data and made it publicly available to the research community. The T. urticae genome sequence reveals herbivorous pest adaptations with strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Moreover, how this pest responds to a changing host environment is shown by deep transcriptome analysis of T. urticae feeding on different plants. Thus, the T. urticae genome sequence opens up new avenues for understanding the evolution of arthropods as well as the fundamentals of plant–herbivore interactions. The next two chapters (Chapter 3 and Chapter 4) present studies on the annotation and evolution of chemosensory receptors (CRs) in three different spider mites. Chemosensory receptors help animals to detect certain chemical components in their environment to find food, to locate shelter, mates and offspring, and to avoid danger. In Chapter 3, starting from Daphnia and insect chemosensory receptors, we describe mining the T. urticae genome for putative chemosensory receptors, including the ones related to insect gustatory receptors (GRs), the ionotropic receptors (IRs) and the epithelial Na+ channels (ENaCs). T. urticae has a huge repertoire of GRs, many more than the total number of GRs and odorant receptors (ORs) found to date in any other arthropod. Similar to Daphnia pulex, we observed the complete lack of ORs in T. urticae. This is consistent with the hypothesis that ORs are an insect-specific class of GR-related chemosensory receptors. Futhermore, we compare chemosensory receptor genes among three strains (London, Montpellier, and EtoxR). We find that GR genes that are intact in some T. urticae populations appeared to be inactived in other populations. Next, in Chapter 4, we describe the annotation of GR genes in T. evansi and T. lintearius, and the evolutionary analysis of this gene family in the three spider mites. We identify many GR gene expansions in the polyphagous T. urticae, a few gene expansions and many gene losses in the oligophagous T. evansi, and no gene expansion but also many gene losses in the monophagous T. lintearius. Finally, general remarks are discussed in the Chapter 5.