Investigating the genomic and phenotypic consequences of recurrent whole genome duplication in spiders

研究蜘蛛中反复出现的全基因组复制的基因组和表型后果

• 批准号: NE/T006854/1
• 负责人: Alistair McGregor
• 金额: $ 59.18万
• 依托单位: Oxford Brookes University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FT006854%2F1
• 关键词: Investigating; genomic; phenotypic; consequences; recurrent

The duplication of genes provides new genetic material that can be used for novel functions, allowing plants and animals to evolve biological innovations and adapt to environmental conditions. Whole genome duplication (WGD) is arguably the most dramatic mechanism for duplication, resulting in the production of a new copy of every gene in the nuclear genome. Around 430 million years ago, spiders and scorpions diverged from a common ancestor that had experienced a WGD. The retained duplicated genes from this WGD event (genes called ohnologs) can still be found in the genomes of the approximately 45,000 species of these animals alive today and may have contributed to their adaptation and diversification. Since then, some families of Synspermiata spiders have undergone at least two additional WGDs within a single lineage, reflecting a similar series of WGDs in vertebrates. This presents an opportunity to compare these events to determine whether there are general principals shaping the outcomes of WGDs and their contribution to animal diversification. In addition, Synspermiata represent a wide diversity of spiders that are understudied and poorly understood Therefore, the aims of this project are to identify spider ohnologs after multiple WGDs, explore whether and how they have contributed to the evolutionary success of these animals, and compare the outcomes of these events to repeated WGDs in vertebrates. We will first collect and carry out the first large scale detailed study of the morphology of Synspermiata spiders to better understand their evolution and phenotypic diversity. In parallel, we will identify the ohnologs that have been retained in spider groups after WGDs by comparing the repertoire and arrangement of the duplicated genes in these animals with relatives where there is no evidence of additional WGDs. As part of this aim, we will sequence the genomes of Synspermiata spiders that have undergone one (Pholcus phalangioides, Scytodes thoracica and Loxosceles reclusa), and two (Oonops pulcher, Segestria senoculata and Dysdera crocata) WGD, as well as the transcriptomes of Caponiidae species with two (Orthonops zebra) or three (Calponia harrisonfordi) WGDs. Since relatively little is known about these spiders this will provide new insights into the biology of these animals as well as their genome evolution. We will then compare the repertoires of genes retained after WGD between spiders and vertebrates to determine whether there are any similarities in the aftermath of these events. This information will help us to better understand the general consequences of WGD and the principles underlying their outcomes in terms of genes being preferentially retained or lost again. Identification of ohnologs will also allow us to ask if these genes have been subject to sub-, neofunctionalisation or specialisation during spider development and if their expression is associated with morphological diversification. Overall our project will provide new insights into the genomes of spiders and how WGDs in these animals have contributed to their morphological evolution. Our data will also allow comparisons to WGD events in other animals, including vertebrates, to better understand the general consequences of these events and their contribution to animal adaptation and diversification.

基因的复制提供了可用于新功能的新遗传物质，使动植物可以发展生物创新并适应环境条件。整个基因组重复（WGD）可以说是重复的最戏剧性机制，导致产生核基因组中每个基因的新副本。大约4.3亿年前，蜘蛛和蝎子与经历过WGD的共同祖先有所不同。该WGD事件中保留的重复基因（称为OHNOLOLS）仍然可以在当今大约45,000种这些动物的基因组中找到，并且可能有助于它们的适应性和多样化。从那时起，一些Synspermiata蜘蛛的家族在单个谱系中至少进行了两个WGD，反映了脊椎动物中类似的WGD系列。这为比较这些事件的机会提供了一个机会，以确定是否有一般校长塑造WGD的结果及其对动物多样化的贡献。此外，Synspermiata代表了多种蜘蛛的多样性，这些蜘蛛被研究且知之甚少，因此，该项目的目的是在多个WGD之后识别蜘蛛OHNOLOLIS，探索它们是否以及如何为这些动物的进化成功做出贡献，并比较这些事件的重复WGD中的WGD中的WGD。我们将首先收集并进行第一个大规模详细研究，以了解Synspermiata蜘蛛的形态，以更好地了解它们的演化和表型多样性。同时，我们将通过比较这些动物中重复的基因的曲目和排列与没有其他WGD的迹象的亲戚，通过比较重复基因的曲目和排列来确定已保留在蜘蛛组中的OHnologs。 As part of this aim, we will sequence the genomes of Synspermiata spiders that have undergone one (Pholcus phalangioides, Scytodes thoracica and Loxosceles reclusa), and two (Oonops pulcher, Segestria senoculata and Dysdera crocata) WGD, as well as the transcriptomes of Caponiidae species with two (Orthonops斑马）或三个（Calponia Harrisonfordi）WGD。由于对这些蜘蛛的了解相对较少，因此可以为这些动物的生物学以及它们的基因组进化提供新的见解。然后，我们将比较蜘蛛和脊椎动物之间WGD后保留的基因的库，以确定这些事件的后果是否有任何相似之处。这些信息将有助于我们更好地了解WGD的总体后果以及其在优先保留或再次丢失基因方面取得结果的原则。 OHNOLOLS的鉴定还将允许我们询问这些基因在蜘蛛发育过程中是否受到亚官能化，新功能化或专业化的约束，以及它们的表达是否与形态学多样化有关。总体而言，我们的项目将为蜘蛛的基因组以及这些动物中的WGD提供新的见解。我们的数据还将允许与包括脊椎动物在内的其他动物中的WGD事件进行比较，以更好地了解这些事件的总体后果及其对动物适应和多样化的贡献。

项目成果

Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

• DOI: 10.1101/2020.07.10.177725
• 发表时间: 1000-01-01
• 期刊: bioRxiv.
• 作者: Harper, A;Baudouin Gonzalez, L;Sumner-Rooney, L
• 通讯作者: Sumner-Rooney, L

The Evolution of Sox Gene Repertoires and Regulation of Segmentation in Arachnids.

• DOI: 10.1093/molbev/msab088
• 发表时间: 2021-07-29
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Baudouin-Gonzalez L;Schoenauer A;Harper A;Blakeley G;Seiter M;Arif S;Sumner-Rooney L;Russell S;Sharma PP;McGregor AP
• 通讯作者: McGregor AP

Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates.

• DOI: 10.1093/g3journal/jkab299
• 发表时间: 2021-12-08
• 期刊: G3 (Bethesda, Md.)
• 作者: Harper A;Baudouin Gonzalez L;Schönauer A;Janssen R;Seiter M;Holzem M;Arif S;McGregor AP;Sumner-Rooney L
• 通讯作者: Sumner-Rooney L

The evolution of Sox gene repertoires and regulation of segmentation in arachnids

蛛形纲动物 Sox 基因库的进化和节段调控

• DOI: 10.1101/2020.06.04.133389
• 发表时间: 2020
• 作者: Baudouin-Gonzalez L