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

基因和基因组复制以及表型新颖性 – 来自蜘蛛和昆虫的见解

• 批准号: 503325252
• 负责人: Dr. Matthias Pechmann
• 金额: --
• 依托单位: Abteilung Entwicklungsbiologie
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/503325252?language=en
• 关键词: Gene; genome; duplication; phenotypic; novelties

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.

表型的新颖性，例如昆虫的翅膀或蜘蛛丝腺的翅膀，促进了对环境变化的适应，因此是进化多样化的主要驱动力。通过小型基因重复（串联重复）或大规模重复（染色体或整个基因组重复）扩展基因组信息是这种新颖性的重要先决条件。最近对不同节肢动物组的基因组分析显示，在蛛网膜的底部至少有一个大规模重复事件（例如蜘蛛和蝎子）。这一发现提供了一个独特的机会，可以将大规模重复事件与在昆虫中通常观察到的小规模重复的后果进行比较。由于脊椎动物（经过了几轮基因组重复），迄今已成为研究大规模重复事件的后果的唯一动物，因此节肢动物中的新基因组资源现在促进了对不同动物组的大规模重复事件的比较。对生物体有益的重复基因通常保留在基因组中，随后的基因表达和功能多样化有助于表型创新。节肢动物中缺少对基因重复的全系统基因组分析及其对表型新颖性的影响。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方法，以揭示昆虫和蜘蛛中的基因保留和基因损失模式，并在功能上测试基因重复对表型新颖性的影响。我们将组装和注释高质量的参考基因组，以占代表性不足的蜘蛛谱系，并将它们与现有的高质量昆虫和螯合基因组一起分析。我们将研究内含子体系结构，可转移元素含量，染色质可及性和转录表表达水平，以洞悉基因副本表达多样化的分子机制。对于选定的基因复制物，我们将分析呼吸器官或丝绸设备等蜘蛛新颖性中的空间和时间表达，以及基因子集的功能将通过RNA干扰介导的基因敲击在功能上验证。我们的工作将为基因和基因组重复的程度，性质和后果提供独特的见解及其对表型新颖性的进化和多样化的重要性。