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

基因的复制提供了可用于新功能的新遗传物质，使植物和动物能够进化出生物创新并适应环境条件。全基因组复制（WGD）可以说是最引人注目的复制机制，导致核基因组中每个基因的新副本的产生。大约4.3亿年前，蜘蛛和蝎子从经历过WGD的共同祖先分化而来。从WGD事件中保留下来的重复基因（称为同源基因）仍然可以在今天存活的大约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和多样化。从那时起，一些纲蛛科在一个谱系中至少经历了两次额外的WGDs，反映了脊椎动物中类似的一系列WGDs。这为比较这些事件提供了一个机会，以确定是否存在影响WGDs结果及其对动物多样化的贡献的一般原则。因此，本项目的目的是鉴定多次WGDs后的蜘蛛技术，探索它们是否以及如何促成这些动物的进化成功，并将这些事件的结果与脊椎动物重复WGDs的结果进行比较。我们将首先收集并开展第一次大规模的详细形态学研究，以更好地了解它们的进化和表型多样性。同时，我们将通过比较这些动物与没有额外WGDs证据的亲缘动物的重复基因的曲目和排列，确定在WGDs后蜘蛛群体中保留的技术。作为这一目标的一部分，我们将测序经过一次（Pholcus phalangioides， Scytodes胸蜘蛛和Loxosceles reclusa）和两次（Oonops pulcher， Segestria senoculata和Dysdera crocata） WGD的合种蜘蛛的基因组，以及具有两次（Orthonops zebra）或三次（Calponia harrisonfordi） WGD的Caponiidae物种的转录组。由于对这些蜘蛛的了解相对较少，这将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在WGD后保留的基因库，以确定这些事件的后果是否有任何相似之处。这些信息将帮助我们更好地理解WGD的一般后果，以及基因被优先保留或再次丢失的基本原则。对同源基因的鉴定也将使我们能够了解这些基因在蜘蛛发育过程中是否受到亚功能化、新功能化或特化的影响，以及它们的表达是否与形态多样化有关。总的来说，我们的项目将为蜘蛛的基因组以及这些动物的WGDs如何促进它们的形态进化提供新的见解。我们的数据还将允许与其他动物（包括脊椎动物）的WGD事件进行比较，以更好地了解这些事件的一般后果及其对动物适应和多样化的贡献。

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.