Bilateral BBSRC-FAPESP. The collision of two genomes: The invasion genomics of Helicoverpa crop pests in Brazil

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 Brazilian 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.

We will study a recent and highly damaging invasive pest species in South America, Helicoverpa armigera, and its ongoing hybridisation with native Helicoverpa zea. The former has a broader host range, a greater propensity to evolve insecticide resistance and is a more pervasive pest, so this represents a major threat to agriculture in the Americas.

We will first generate improved reference genomes for both species using a novel trio-based approach combined with long read sequencing technology. This will generate high quality haploid reference genomes that will be scaffolded to chromosomal level using Hi-C data. Next we will sample moths extensively across Brazil, and sequence genomes from 1000 individuals in order to monitor the invasion and ongoing patterns of hybridisation.

We will pioneer a novel sequencing technology known as 'haplotagging', which obtains long range haplotype information from a cheap Nextera-like library preparation protocol. This will be one of the first large scale population genomics projects that uses this technology, which will provide greatly improved haplotype information for identification of hybrid genome tracts and for demographic inference.

We will use statistical analyses of admixed genomes to identify gene combinations that are under- and over-represented in hybrids and therefore subject to selection as incompatibilities between the divergent genomes. Finally, we will also search for signatures of selective sweeps in both species, using SweepFinder2, VolcanoFinder and alternative machine learning approaches, in order to investigate regions subject to positive selection. These will be candidate loci for adaptation to crop plants and local conditions in both the native and invasive species.

Agricultural pests are a major challenge to global food security, and are increasing in prevalence as invasive pest species colonise new areas of the globe. The moth Helicoverpa armigera is one of the most damaging crop pests worldwide, with a wide host range and an alarming propensity to evolve insecticide resistance. Here we will provide critical information on the invasion of this pest into South America and its hybridisation with a close relative Helicoverpa zea. This project therefore fits clearly in the BBSRC strategic goal of 'Agriculture and Food Security Research' and the focus area of 'Understanding and exploiting genomics'. The impact of the project will have specific benefits in the management of Helicoverpa, and broader implications for improving our understanding of the process of hybridisation during species invasions.

Our study will identify the extent and spread of the Ha invasion of Brazil, and the degree to which insecticide resistance has spread from Ha into Hz across Brazil. We will also identify potential targets of selection in the genomes of both species that could be responsible for adaptation to local conditions in Brazil and to local crop hosts. Correctly understanding the distribution, resistance status and host adaptations in these two species will aid in correct control strategies for future management of these pests.

In order to maximise the impact of the project we will organise two events to which industry partners are invited to disseminate results and discuss implications for control of this major crop pest. The first will be associated with the ESA meeting in the US and the second hosted by us in Brazil. Our connections through Project Partners in CSIRO and Brazil will ensure that representatives from Bayer, BASF, Syngenta, Corteva, commodity groups, FAO, and the USDA, will attend these meetings.

In addition, we will generate genomic resources that will facilitate future work on Helicoverpa including chromosomal level genome assemblies for the two species, and a large resequence data set from populations primarily in Brazil but also from around the world. This will provide important information on genetic variation including structural variation in the genomes that will facilitate future work on these species. These resources will be made publicly available for use by industry and academic partners alike. We will also work with Brazilian partners to develop cheap PCR-based assays for monitoring insecticide resistance and the spread of potentially novel hybrid genotypes.

Hybridisation between pest species during invasions of new ranges is likely to be an increasing problem in a globalised world. We aim for this project to highlight the importance of this process among the academic and agricultural community, in order to promote future research in this area. In summary this project will improve our understanding of a major global crop pest, as well as highlighting the importance of genetic processes that can aid in invasive species expansions.