Gene and genome duplication and phenotypic novelties – Insights from spiders and insects

表型新颖性，如昆虫的翅膀或蜘蛛的丝腺，有助于适应不断变化的环境，因此是进化多样化的主要驱动力。通过小规模基因复制(串联复制)或大规模复制(染色体或全基因组复制)来扩展基因组信息是实现这种新颖性的重要先决条件。最近对不同节肢动物群体的基因组分析显示，蜘蛛类(如蜘蛛和蝎子)的底部至少发生了一次大规模复制事件。这一发现提供了一个独特的机会，可以将大规模复制事件的后果与通常在昆虫中观察到的小规模复制事件的后果进行比较。由于脊椎动物(经历了几轮全基因组复制)是迄今为止唯一研究大规模复制事件后果的动物，节肢动物中的新基因组资源现在有助于比较不同动物群体的大规模复制事件。对生物体有益的复制基因通常保留在基因组中，随后基因表达和功能的多样化有助于表型创新。节肢动物缺乏对基因复制及其对表型新颖性的影响的系统的全基因组分析。因此，我们将结合比较基因组学、功能基因组学和功能遗传学的方法，揭示昆虫和蜘蛛的基因保留和基因丢失模式，并从功能上测试基因复制对表型新颖性的影响。我们将汇编和注释未被充分代表的蜘蛛谱系的高质量参考基因组，并将它们与现有的高质量昆虫和海龟基因组一起进行分析。我们将研究内含子结构、转座元件含量、染色质可及性和转录本表达水平，以深入了解基因重复表达多样化的分子机制。对于选定的基因重复，我们将分析蜘蛛新奇事物(如呼吸器官或丝器)的时空表达，并将通过RNA干扰介导的基因敲除从功能上验证基因子集的功能。我们的工作将为基因和基因组复制的范围、性质和后果以及它们对表型新颖性的进化和多样化的重要性提供独特的见解。

Phenotypic novelties, such as the wings in insects or silk glands in spiders, facilitate adaptations to changing environments and are thus a major driver for evolutionary diversification. Expansion of genomic information by small-scale gene duplications (tandem duplications) or large-scale duplications (chromosomal or whole genome duplications) are important prerequisites for such novelties. Recent genomic analyses of different arthropod groups revealed at least one large scale duplication event at the base of the arachnopulmonates (e.g. spiders and scorpions). This finding provides a unique opportunity to compare the consequences of large-scale duplication events to small-scale duplications commonly observed in insects. Since vertebrates (that underwent several rounds of whole genome duplications), have hitherto been the only animals to study the consequences of large-scale duplication events, new genomic resources in arthropods now facilitate the comparison of large-scale duplication events across different animal groups. Duplicated genes that are beneficial for the organism are usually retained in the genome and subsequent diversification of gene expression and function contributes to phenotypic innovations. A systematic genome-wide analysis of gene duplications and their impact on phenotypic novelties is missing in arthropods. Therefore, we will combine comparative genomics, functional genomics and functional genetics approaches to reveal gene retention and gene loss patterns in insects and spiders and to functionally test the impact of gene duplications on phenotypic novelties. We will assemble and annotate high-quality reference genomes for underrepresented spider lineages and analyze them together with existing high-quality insect and chelicerate genomes. We will study intron architecture, transposable element content, chromatin accessibility and transcript expression levels to gain insights into the molecular mechanisms underlying the diversification of expression of gene duplicates. For selected gene duplicates we will analyze spatial and temporal expression in developing spider novelties like breathing organs or the silk apparatus, and the function of a subset of genes will be functionally validated via RNA interference mediated gene knock-down. Our work will provide unique insights into the extent, nature and consequences of gene and genome duplications and their importance for the evolution and diversification of phenotypic novelties.