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面临的一个重大挑战，给农业带来了巨大的经济成本。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。这可能会有各种潜在的结果：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。另一种情况是，如果两个物种保持完整性，它们可能交换基因，可能使适应新范围的基因促进入侵物种，并使与害虫有关的性状基因进入本地物种。我们将研究这些现象在具有经济破坏性的作物害虫Helicoverpa armigera中，该害虫最近入侵并与巴西本地物种Helicoverpa zea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，对入侵进行大规模的时间和地理监测。我们将使用一种新的测序方法来获取这两个物种的大量种群样本的基因组数据，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的多种来源，最后，杂交对两个物种的遗传后果是什么。为了实现这些目标，我们将首先为这两个物种产生高质量的基因组组装，组装到染色体水平。这将为今后社区用于遗传操作和更广泛地了解这些重要的作物害虫提供资源。这两个物种已经在异种中分化了一百多万年，因此它们之间的遗传差异意味着我们将有相当大的能力来识别两个物种基因组中由物种之间的遗传混合（基因渗入）造成的片段。这些块的大小和分布提供了自杂交以来的时间信息。我们还将通过寻找杂交中未被充分代表的基因组合，确定是否有证据表明两个基因组之间存在不相容，这将有助于在杂交混合的情况下保持它们的独特性。相反，比偶然预期更常见的区域将表明适应性渐渗。在巴西，参与适应当地条件的基因可能会转移到入侵物种中，或者杀虫剂抗性基因可能会从入侵者转移到本地物种中。最后，我们将在这两个物种的种群中寻找近期适应的特征，这些特征可能表明涉及宿主适应、杀虫剂抗性或其他潜在经济重要性特征的基因组区域。特别是，与Hz相比，Ha对更广泛的杀虫剂和寄主物种产生了抗性，因此等位基因的进一步渗入可能会导致Hz的寄主范围扩大和杀虫剂抗性。相比之下，Hz适应巴西的当地条件，并可能提供等位基因，促进对入侵Ha种群的当地适应。该项目将发现可以立即应用于控制这种害虫的模式，例如对入侵者进入新地区的预警，以及识别可能在两个物种之间转移的特征，如杀虫剂抗性。此外，我们将讨论与物种形成生物学相关的基本问题，例如保持物种不同的基因组不相容的性质。

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.