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

入侵性作物害虫是我们这个时代的主要挑战，并导致农业的巨大经济成本。这种入侵的一个不太为人所知的方面是，入侵物种经常与相关的本地物种杂交。这可能有各种潜在的结果：一种可能性是杂交导致物种屏障的崩溃和单一的混合种群。或者，如果这两个物种保持其完整性，它们仍然可以交换基因，可能允许适应新范围的基因促进入侵物种，以及与害虫相关的性状的基因进入本地物种。我们将研究这些现象在经济上毁灭性的农作物害虫棉铃虫，最近入侵，并在巴西与本地物种玉米棉铃虫杂交。与巴西项目合作伙伴一起，我们将通过大规模全基因组测序，对大规模入侵进行时间和地理监测。我们将使用一种新的测序方法来获得这两个物种的大样本种群的基因组数据，这将使我们能够解决以下问题：入侵物种传播的程度和速度是什么，杂交事件的年龄是什么，是否有证据表明入侵者有多个来源，最后是什么两个物种杂交的遗传后果。为了实现这些目标，我们将首先为两个物种生成高质量的基因组组装，组装到染色体水平。这将为未来的遗传操作和更广泛地更好地了解这些重要的作物害虫提供资源。这两个物种在异地分布中已经分化了100多万年，因此它们之间的遗传差异意味着我们将有相当大的力量来识别两个物种基因组中的块，这些块是由物种之间的遗传混合（渐渗）造成的。这些块的大小和分布提供了关于杂交以来的时间的信息。我们还将确定是否有证据表明两个基因组之间的不相容性，这将有助于保持其独特性，在面对混合通过杂交，通过寻找在杂交中代表性不足的遗传组合。相反，比预期的更常见的区域可能表明适应性渐渗。这很可能是因为参与适应巴西当地条件的基因可能会进入入侵物种，或者杀虫剂抗性基因可能会从入侵者进入本地物种。最后，我们将寻找这两个物种的人口，这可能是指示基因组区域参与宿主适应，杀虫剂抗性或其他潜在的经济重要性的特征最近的适应签名。特别是，Ha已开发出更广泛的杀虫剂和宿主物种相比，Hz的抗性，所以有可能进一步渗入的等位基因，可能会沉淀主机范围扩大和杀虫剂抗性Hz。与此相反，Hz是适应当地条件在巴西，并可能借给等位基因，促进当地适应入侵的哈population.The项目将揭示模式，将立即应用于控制这种害虫，例如预警的入侵者进入新的地区的到来，并确定特性，如杀虫剂抗性比可以在两个物种之间转移。此外，我们将解决有关物种形成生物学的基本问题，如保持物种独特的基因组不相容性的性质。

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.