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

互惠-物种之间的合作-是无处不在的，并与生命历史上的重大转变有关，例如真核生物的进化或植物对土地的征服。它们使新的谱系多样化，使物种能够获得否则无法获得的资源，并从根本上改变了地球的地球化学循环。然而，理解互惠依赖的起源和进化轨迹仍然是一个重大挑战。除了微生物内共生体之外，共生互惠体如何影响基因组还知之甚少。本计画拟探讨在最大的蚂蚁/植物共生系统中，互惠相依如何影响与进化互动相关的基因。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，在咖啡植物家族（Rubiaceae）的Hydnophytinae分支是唯一复制：专业化和互惠共生的损失发生反复在该组的进化历史。在红皇后假说动力学之后，专性依赖是否促进了更快的分子进化速率？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？互惠依赖的完全丧失是否会导致共生基因的退化？使用一个独特的复制系统，大量的互惠分解（规模缩放），学生将测试这些替代假设。目的学生将进行比较基因组分析，并在整个Hydnophytinae进化枝（~105种）和适当的外类群的基因组分析。一个共生工具包的基因的利益将确定使用转录组学和全基因组序列在手。学生将使用靶向杂交捕获基于100个基因（质体加数百个核基因）生成一个坚实的基因组数据集。然后，学生将重建与共生关系（如氮和磷转运蛋白）相关的主要基因家族的进化，并重建它们的系统发育历史，揭示基因家族的损失和扩张以及共生互利关系的经常性损失或专业化。使用该数据集，学生将在进化枝中进行选择测试，重点关注（i）靶向基因家族和（ii）使用互补方法的全基因组分析，以测试竞争假设。方法本项目将使用（i）基于靶向测序的共生基因组学，（ii）比较基因组学，使用（1）120个物种的“共生工具包”的靶向测序，（2）20个物种的全基因组测序和（iii）使用互补方法的选择测试。活动时间表第一年：生成所有序列数据，熟悉组的系统性。第二年：生成物种遗传学，关键基因家族的遗传学，组装全基因组数据。第三年：完成基因组分析并撰写论文。新奇提出的博士项目是及时的几个原因：基因组学的出现与测序方法和计算工具现在允许非模式，野生物种的基因组组装;（3）Hydnophytinae是一个很有前途的系统，研究进化和生态学的互利共生在各种规模，因为它的高度复制的历史。这个项目也是新颖的，因为：（1）它将提供一个新的阅读的多样性的互惠通过一个基本的，统一的方面：依赖;（2）互惠的比较基因组学是一个新兴的（外与微生物的内共生），非常有前途的研究领域。学生培训学生将接受以下方面的培训：（1）下一代测序的分子方法;（2）基因组学;（3）基因组分析（基因组组装、基因选择测试、全基因组基因选择）。

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).