Know your enemy : Genomes of biological control agents

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Biological control is the use of an organism, the biological control agent (BCA), to control the population of another organism, the pest. While BCAs are used around the world and in a variety of agricultural contexts, increasing the uptake would be beneficial to key goals of sustainable agriculture. To do so, there is the desire for improving BCAs, either in terms of their production, their performance, or the reduction of non-target effects after release. One way to improve BCAs is to use a genetics approach with next-generation sequencing and genomics. The study of genetics is essentially about evolution and inheritance, and its application on BCAs is straightforward: are the traits that we are interested in, such as parasitism rate for parasitoid wasps or starvation resistance for predatory bugs, 1) heritable, and 2) able to be improved without deleterious (side-)effects? Is there enough genetic variation within a population to select for improvement of these traits? While these scenarios can be used for improving the BCAs themselves, the way that BCAs are monitored, stored, and assessed for non-target effects can also be improved using genetics and/or genomics. This thesis and the work within involved generating genomic results and resources for five biological control agents (including a predatory mite, two parasitoid wasps, and a predatory mirid bug), complete with context and suggestions for future directions. This thesis is also intended to act as a sort of guidebook for biological control practitioners considering genome projects. The introduction (Chapter 1) begins with defining an anthology, and the intention to treat this thesis as such. After introducing concepts of biological control, genetics and genomics, and the international project behind this thesis (BINGO-ITN), the research chapters begin. Chapter 2 contains a systematic review of biological control literature centered on documenting the amount of genetic variability research on BCAs, ending with a call for more rigorous reporting of variables such as heritability and evolvability. Chapter 3 contains a previously published work on whole genome sequencing via nanopore MinION technology and resulting microsatellite generation and population genetics of the predatory mite, Amblyseius swirskii. Chapter 4 and Chapter 5 are both in the style of genome reports, reduced-length manuscripts that, while destined for peer-review, are more straight to the point of describing genomes and any resulting analyses. Chapter 4 is the linked-read de novo annotated genome of parasitoid wasp Bracon brevicornis and resulting analyses into a putative region related to complementary sex determination, a defining feature of this parasitoid. Chapter 5 contains the hybrid de novo annotated genome of parasitoid wasp Trichogramma brassicae, where long- and short-read technology were used on a strain that was aided in its homozygosity by a Wolbachia infection. Chapter 6 features population studies and builds upon the reads generated in Chapter 5 by mining microsatellites from the short-reads to be used upon wild-caught lines of sister species Trichogramma evanescens. These German-origin lines were compared in a variety of ways using population genetics (the aforementioned microsatellites) as well as population genomics via pooled sequencing analyses and a de novo (unannotated) genome. Chapter 7, the final research chapter, contains the linked-read de novo annotated genome of predatory mirid Nesidiocoris tenuis, an important BCA used throughout the Mediterranean that is also considered a pest in other areas of the world. In addition to the genome, additional analyses include bacterial decontamination (leading to putative symbiont identification), potential lateral gene transfer events (though it is difficult to qualify initially), population genomics, and cytogenetic investigations into karyotype, sex determination system, unique satellites, and the presence/absence of the insect ancestral telomeric motif. This variety of investigations offer a taste of what is possible with a genome, acting as inspiration for future research. The thesis/anthology is wrapped up in Chapter 8, the synthesis, where the preceding research chapters are examined in the light of themes presented in the introduction, and more general notes over the success (or failure?) of these various projects. Appendices contain four summaries (English, Dutch, German, and Spanish) as well as Acknowledgements, About the Author, and About the Artwork found within the thesis (each chapter title has a unique accompanying illustration).