The collision of two genomes: the invasion genomics of Helicoverpa crop pests in Brazil

Abstract

Invasive crop pests are a major challenge of our times, and lead to huge economic costs to agriculture. One less well recognised aspect of such invasions is that invasive species often hybridise with related native species. This can have various potential outcomes: One possibility is that hybridisation leads to a collapse of the species barrier and a single mixed population. Alternatively, if the two species maintain their integrity they may nonetheless exchange genes, potentially allowing genes for adaptation to the novel range to facilitate the invasive species, and genes for pest-related traits to enter the native species. We will study these phenomena in the economically devastating crop pests Helicoverpa armigera, which has recently invaded and is hybridising with a native species Helicoverpa zea in Brazil. With Project Partners we will conduct temporal and geographic monitoring of the invasion across a large scale, facilitated by large scale whole genome sequencing. We will use a novel sequencing approach to obtain genomic data for a large sample of populations of both species, which will allow us to address the following questions: What is the extent and speed of spread by the invasive species, what is the age of the hybridisation event and is there evidence for multiple sources of invaders, and finally what are the genetic consequences of hybridisation for the two species. In order to achieve these goals we will first generate high quality genome assemblies for both species, assembled to chromosomal level. This will provide resources that will be used by the community in the future for genetic manipulation and more broadly gaining a better understanding of these important crop pests. The two species have diverged in allopatry for over a million years, so genetic differences between them mean that we will have considerable power to identify blocks in the genomes of both species that have resulted from genetic mixing between the species (introgression). The size and distribution of these blocks provides information about the time since hybridisation. We will also determine whether there is evidence for incompatibilities between the two genomes that would help to maintain their distinctiveness in the face of mixing through hybridisation, by looking for genetic combinations that are under-represented in hybrids. In contrast regions that are more common than expected by chance would indicate adaptive introgression. This is likely for genes involved in adaptation to local conditions in Brazil that may move into the invasive species, or genes for insecticide resistance that are likely to move into the native species from the invader. Finally, we will search for signatures of recent adaptation in the populations of both species, which might be indicative of genomic regions involved in host adaptation, insecticide resistance or other traits of potential economic importance. In particular, Ha has developed resistance to a far wider range of insecticides and host species as compared to Hz, so there is potential for further introgression of alleles that could precipitate host range expansion and insecticide resistance in Hz. In contrast, Hz is adapted to local conditions in Brazil and might lend alleles that facilitate local adaptation to the invasive Ha populations. The project will uncover patterns that will be of immediate application in the control of this pest, for example forewarning of the arrival of the invader into new areas, and identifying characteristics such as insecticide resistance than could be transferred between the two species. In addition, we will address fundamental questions related to speciation biology, such as the nature of the genomic incompatibilities that keep species distinct. (AU)