The impact of mutualistic dependence on the evolution interaction-related genes: a case study in the largest ant/plant symbiotic system

互利依赖对进化相互作用相关基因的影响：最大的蚂蚁/植物共生系统的案例研究

• 批准号: 2369271
• 金额: --
• 依托单位: Durham University
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2369271
• 关键词: impact; mutualistic; dependence; evolution; interaction

Background Mutualisms -cooperation between species- are ubiquitous and linked to major transitions in the history of life, such as the evolution of eukaryotes or the conquest of the land by plants. They have allowed the diversification of new lineages, permitted species to access otherwise inaccessible resources and radically modified Earth's geochemical cycles. Yet, understanding the origins and evolutionary trajectories of mutualistic dependences remains a major challenge. How symbiotic mutualisms impact genomes is poorly known besides microbial endosymbioses. This project proposes to test how mutualistic dependence influences the evolution interaction-related genes in the largest ant/plant symbiotic system. The symbiotic system involves epiphytic plants offering lodging and sometimes food to ants in return for extra nutrients and sometimes defense against herbivores. This system, the Hydnophytinae clade in the coffee plant family (Rubiaceae) is uniquely replicated: specialization and loss of the mutualism occurred recurrently over the group's evolutionary history. Does obligate dependence promote faster rates of molecular evolution following a Red Queen Hypothesis dynamics? Or alternatively, do they rather show evolutionary stasis as predicted if there is no conflict with the partner? Does the complete loss of mutualistic dependence lead to the degradation of symbiotic genes? Using a uniquely replicated system, with a large number of mutualism breakdowns (scaled to size), the student will test these alternative hypotheses. Aims The student will conduct comparative genomic analyses and phylogenomic analyses across the whole Hydnophytinae clade (~105 species) and appropriate outgroups. A symbiotic toolkit of genes of interest will be identified using transcriptomics and whole genome sequences at hand. The student will generate a solid phylogenomic dataset based on 100s genes (plastome plus hundreds of nuclear genes) using targeted hybrid capture. The student will then reconstruct the evolution of major gene families linked to the mutualism such as nitrogen and phosphorus transporters, and reconstruct their phylogenetic history, unveiling loss and expansions of gene families together with recurrent loss or specialization of the symbiotic mutualism. Using this dataset, the student will perform selection tests across the clade, focusing both on (i) targeted gene families and (ii) genome-wide analyses using complementary approaches, to test the competing hypotheses.Methodology This project will use (i) targeted-sequencing-based phylogenomics, (ii) comparative genomics using (1) targeted sequencing of a 'symbiotic toolkit' across 120 species, (2) whole genome sequencing for 20 species and (iii) selection tests using complementary methods. Timetable of Activities Year 1: Generate all sequence data, becoming familiar with the systematics of the group. Year 2: Generate species phylogeny, and phylogenies for key gene families, assemble whole genome data. Year 3: Finish genomic analyses and write up thesis.Novelty The proposed PhD project is timely for several reasons: the advent of genomics with both sequencing methods and computational tools now allow genome assembly for non-model, wild species; (3) the Hydnophytinae are a promising system to study evolution and ecology of mutualism at various scales because of its highly replicated history. This project is also novel because: (1) it will provide a new reading of the diversity of mutualisms through an essential, unifying aspect: dependence; (2) the comparative genomics of mutualisms is an emerging (outside endosymbioses with microbes), highly promising research field. As a result, I anticipate that this will result in several high-profile publications.Student Training The student will receive training in (1) molecular methods for next-generation sequencing; (2) phylogenomics; (3) genomic analyses (genome assembly, gene selection test, genome-wide gene selection).

互利共生——物种之间的合作——无处不在，与生命史上的重大转变有关，如真核生物的进化或植物对土地的征服。它们使新世系得以多样化，使物种得以获得原本无法获得的资源，并从根本上改变了地球的地球化学循环。然而，了解相互依存的起源和进化轨迹仍然是一个重大挑战。除了微生物内共生外，我们对共生互惠如何影响基因组知之甚少。本项目拟在最大的蚂蚁/植物共生系统中测试互惠依赖如何影响进化相互作用相关基因。共生系统包括附生植物提供住宿，有时为蚂蚁提供食物，以换取额外的营养，有时防御食草动物。这个系统，咖啡植物家族（Rubiaceae）中的水phytinae分支是独特的复制：专业化和互惠关系的丧失在该群体的进化史上反复发生。强制性依赖是否促进了红皇后假说下更快的分子进化速度？或者，如果与伴侣没有冲突，他们是否会像预测的那样表现出进化停滞？相互依赖的完全丧失会导致共生基因的退化吗？使用一个独特的复制系统，与大量的互惠崩溃（按比例缩放），学生将测试这些替代假设。该学生将对整个藻门分支（约105种）和适当的外群进行比较基因组分析和系统基因组分析。将利用转录组学和全基因组序列识别感兴趣的基因的共生工具包。该学生将使用靶向杂交捕获技术生成基于100个基因（质体体加上数百个核基因）的固体系统基因组数据集。然后，学生将重建与共生关系相关的主要基因家族的进化，如氮和磷转运体，重建它们的系统发育历史，揭示基因家族的丢失和扩展，以及共生互惠关系的反复丢失或专门化。使用此数据集，学生将在进化枝上进行选择测试，重点关注(i)目标基因家族和（ii）使用互补方法进行全基因组分析，以测试相互竞争的假设。该项目将使用(i)基于靶向测序的系统基因组学，（ii）比较基因组学，使用(1)对120个物种的“共生工具包”进行靶向测序，(2)对20个物种进行全基因组测序，（iii）使用互补方法进行选择测试。活动时间表一年级：生成所有序列数据，熟悉集团的系统。第2年：生成物种系统发育和关键基因家族的系统发育，组装全基因组数据。第三年：完成基因组分析并撰写论文。提出的博士项目是及时的，有几个原因：基因组学的出现与测序方法和计算工具现在允许非模型的基因组组装，野生物种；(3)藻门具有高度可复制的历史，是研究不同尺度共生进化和生态的一个有前景的系统。这个项目也是新颖的，因为：(1)它将通过一个基本的、统一的方面提供对互惠关系多样性的新解读：依赖性；(2)互惠共生的比较基因组学是一个新兴的（与微生物外共生的）、极具发展前景的研究领域。因此，我预计这将导致一些备受瞩目的出版物。学员培训学员将接受以下方面的培训：(1)下一代测序的分子方法；(2) phylogenomics;(3)基因组分析（基因组组装、基因选择检验、全基因组基因选择）。