Genomic and gene regulatory basis of rapid evolutionary diversification of a multifunctional trait

进化创新可以由各种机制引起，例如基因内的突变、编码蛋白质的基因从非编码DNA从头进化、基因复制、可转座元件的插入以及基因转录速率的变化(即调节变化)。进化创新对研究复杂的表型特征特别有趣，这些表型特征对有机体至关重要，但进化很快。其中一个特征是昆虫的角质碳氢化合物(CHC)分布。CHC覆盖了几乎所有昆虫的身体，防止水分流失，并在化学交流中发挥作用。CHC谱可能在密切相关的物种之间，甚至在同种性别或社会昆虫种姓之间差异很大，这表明潜在的遗传机制是多种多样的。有趣的是，在膜翅目昆虫中，相似的CHC表型也反复进化。尽管我们对CHC的一般生物合成途径有了一定的了解，但我们仍然对CHC种内和种间变异以及新的表型背后的分子进化机制知之甚少。我们的项目旨在确定CHC多样化的基因组、转录和表观遗传学基础。我们将研究13对密切相关但化学上不同的物种，它们几乎涵盖了有刺的膜翅目的所有主要谱系(刺蜂、蚂蚁和蜜蜂)。此外，还将研究这26个物种中的10个物种的性别和种姓差异。应用跨物种比较基因组学方法，我们将评估基因拷贝数变化、编码序列中的非同义变化、选择性mRNA剪接和其他调节变化对促进表型差异的相对重要性。我们将调查基因拷贝数变异是否由异位重组或转座元件的活性所促进。最后，我们将评估CHC生物合成基因的亚组是否已经进化成协同调节单位，这可能解释了相似表型的快速表型变异和重复进化。为此，我们将获得组织特异性转录本。我们还将通过ATAC-SEQ的开放染色质图谱与通过全基因组亚硫酸氢盐测序的甲基化模式进行比较，以确定表观遗传机制在调控CHC变异中的作用。我们假设，亲缘关系密切的物种之间的CHC谱差异是由与同种性别或种姓之间的差异类似的机制驱动的。我们预计基因组机制，如核苷酸分歧和基因拷贝数变异(包括。新功能化)，主要是造成远亲物种之间的差异。我们的结果将有助于更好地理解塑造高度可变但至关重要的表型性状进化的分子机制。因此，我们将对多种基因组和基因调控机制的相互作用如何实现进化创新和多样化获得新的见解。

Evolutionary innovation can result from various mechanisms, such as mutations within genes, de novo-evolution of protein-coding genes from non-coding DNA, gene duplication, insertions of transposable elements, and changes in the transcription rate of genes (i.e., regulatory change). Evolutionary innovation is particularly interesting to study on complex phenotypic traits that are vital for the organism, yet evolve rapidly. One such trait is the cuticular hydrocarbon (CHC) profile of insects. CHCs cover the body of essentially all insects, protecting against water loss and functioning in chemical communication. CHC profiles can vary drastically between closely related species or even between conspecific sexes or social insect castes, suggesting a versatile underlying genetic machinery. Interestingly, in the insect order Hymenoptera, similar CHC phenotypes have evolved repeatedly. Despite some understanding of the general CHC biosynthesis pathways, we still know little about the molecular evolutionary mechanisms behind intra- and interspecific CHC variation and novel phenotypes. Our project aims at identifying the genomic, transcriptomic, and epigenetic underpinnings of CHC diversification. We will study 13 pairs of closely related yet chemically different species that cover almost all major lineages of aculeate Hymenoptera (stinging wasps, ant, and bees). Sex and caste differences will additionally be studied in ten of these 26 species. Applying a cross-species comparative genomic approach, we will assess the relative importance of gene copy number variation, non-synonymous changes in coding sequences, alternative mRNA splicing, and other regulatory changes for fostering phenotypic divergence. We will investigate whether gene copy number variation has been promoted by ectopic recombination or the activity of transposable elements. Finally, we will evaluate whether subgroups of CHC biosynthesis genes may have evolved into superordinated co-regulated units, potentially explaining rapid phenotypic variation and repeated evolution of similar phenotypes. To this end, we will obtain tissue-specific transcriptomes. We will also contrast open chromatin maps via ATAC-seq to methylation patterns via whole genome bisulfite sequencing to determine the role of epigenetic mechanisms in regulating CHC variation. We hypothesize that CHC profile divergence between closely related species is driven by similar mechanisms as the divergence between conspecific sexes or castes. We expect genomic mechanisms, such as nucleotide divergence and gene copy number variation (incl. neofunctionalization), to primarily cause divergence between distantly related species. Our results will contribute to a better understanding of the molecular mechanisms that shape the evolution of a highly variable yet vital phenotypic trait. Thus, we will gain new insights into how the interplay of multiple genomic and gene regulatory mechanisms enables evolutionary innovation and diversification.