Genomic traces of symbiosis loss A symbiosis between certain bacteria and their plant hosts delivers fixed nitrogen to the plants. Griesmann et al. sequenced several plant genomes to analyze why nitrogen-fixing symbiosis is irregularly scattered through the evolutionary tree (see the Perspective by Nagy). Various genomes carried traces of lost pathways that could have supported nitrogen-fixing symbiosis. It seems that this symbiosis, which relies on multiple pathways and complex interorganismal signaling, is susceptible to selection and prone to being lost over evolutionary time. Science, this issue p. eaat1743; see also p. 125 Genome-wide comparative analysis across species reveals the fragility of the plant-bacterial symbiosis needed for nitrogen fixation. INTRODUCTION Access to nutrients such as nitrogen is required for plant growth. Legumes and nine additional plant families benefit from the nitrogen-fixing root nodule (NFN) symbiosis, in which roots develop nodules that intracellularly host nitrogen-fixing bacteria. In this mutually beneficial symbiosis, the bacteria convert atmospheric nitrogen into ammonium and deliver it to the host plant. NFN symbiosis thus enables plant survival under nitrogen-limiting conditions in terrestrial ecosystems. In agriculture, this symbiosis reduces reliance on nitrogen fertilizer, thus reducing the costs, ecological impact, and fossil fuel consumption attendant on large-scale application of fertilizers. RATIONALE Molecular phylogenies show that NFN symbiosis is restricted to four angiosperm orders—Fabales, Fagales, Cucurbitales, and Rosales—that together form the monophyletic NFN clade. However, only 10 of the 28 plant families within this clade contain species engaged in the NFN symbiosis. Even within these 10 families, most genera do not form this symbiosis. The NFN symbiosis requires the coordinated function of more than 30 essential genes. Presence of this symbiosis in related families suggests that a genetic change in the ancestor of the NFN clade enabled evolution of NFN symbiosis in this clade. The scattered distribution of functional NFN symbiosis across the clade has led to the question of whether NFN symbiosis evolved multiple times independently in a convergent manner or was lost multiple times regardless of the number of times it arose. Fossil data have been unable to answer this question. Here we used molecular evidence to ask how the current pattern of plant species with NFN symbiosis evolved. RESULTS We sequenced the genomes of seven nodulating species belonging to the Fagales, Rosales, and Cucurbitales orders and the legume subfamily Caesalpinioideae. We complemented this dataset by sequencing three genomes of nonnodulating species from the Cucurbitales and from the legume subfamilies Cercidoideae and Papilionoideae. Using a genome-wide phylogenomic approach, we found that all legume genes with a characterized role in NFN symbiosis are conserved in nodulating species with one exception. We observed larger numbers of order-specific gene family expansions that, solely because of their phylogenetic distribution, may include genes contributing to multiple gains or subsequent refinements of the symbiosis. In parallel, we discovered signatures of multiple independent loss-of-function events for the gene encoding the indispensable NFN symbiosis regulator NODULE INCEPTION (NIN) in 10 of 13 genomes of nonnodulating species within the NFN clade. The pattern suggests at least eight independent losses of NFN symbiosis. CONCLUSION We found that multiple independent losses of NFN symbiosis occurred in the four orders of the NFN clade. These results suggest that NFN symbiosis has previously been more common than currently evident and that this symbiosis is subject to an underestimated adverse selection pressure. Phylogenomics and evolution of NFN symbiosis. Genome sequencing of nodulating and nonnodulating species combined with 27 previously available genomes resulted in a dataset spanning the NFN clade and species outside the NFN clade as an outgroup. Orthogroups were identified and filtered following three phylogenetic patterns. This genome-wide analysis identified two genes involved in NFN symbiosis, NIN and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG), that were lost in most nonnodulating species. The occurrence of multiple losses (red crosses) of NFN symbiosis suggests an adverse selection pressure. The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.

中文翻译：

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系统基因组学揭示了固氮根瘤共生的多重丧失

共生丧失的基因组痕迹某些细菌与其植物宿主之间的共生为植物提供了固定的氮。格里斯曼等人。对几个植物基因组进行测序，以分析为什么固氮共生不规则地分散在进化树中（参见 Nagy 的观点）。各种基因组携带了可能支持固氮共生的丢失途径的痕迹。似乎这种依赖于多种途径和复杂的有机体间信号的共生很容易受到选择的影响，并且在进化过程中容易丢失。科学，这个问题 p。eaat1743; 另见第。125 跨物种的全基因组比较分析揭示了固氮所需的植物-细菌共生的脆弱性。引言 植物生长需要获取氮等养分。豆科植物和另外九个植物科受益于固氮根瘤 (NFN) 共生，在这种共生中，根部会形成可在细胞内寄宿固氮细菌的根瘤。在这种互惠互利的共生关系中，细菌将大气中的氮转化为铵并将其输送给寄主植物。因此，NFN 共生使植物能够在陆地生态系统中的氮限制条件下生存。在农业中，这种共生减少了对氮肥的依赖，从而降低了大规模施用化肥所带来的成本、生态影响和化石燃料消耗。基本原理分子系统发育表明，NFN 共生仅限于四个被子植物目——Fabales、Fagales、Cucurbitales 和 Rosales——它们共同形成了单系 NFN 进化枝。然而，在这个进化枝中的 28 个植物科中，只有 10 个包含参与 NFN 共生的物种。即使在这 10 个科中，大多数属也没有形成这种共生关系。NFN 共生需要 30 多个必需基因的协调功能。这种共生在相关家族中的存在表明 NFN 进化枝祖先的遗传变化使该进化枝中 NFN 共生的进化成为可能。功能性 NFN 共生在整个进化枝中的分散分布导致了一个问题，即 NFN 共生是以收敛方式独立进化多次还是无论出现多少次都丢失多次。化石数据一直无法回答这个问题。在这里，我们使用分子证据来询问当前与 NFN 共生的植物物种模式是如何进化的。结果我们对属于 Fagales、Rosales 和 Cucurbitales 目以及豆科植物 Caesalpinioideae 的七个根瘤物种的基因组进行了测序。我们通过对来自葫芦科和豆科植物 Cercidoideae 和 Papilionoideae 的非结瘤物种的三个基因组进行测序来补充该数据集。使用全基因组系统基因组学方法，我们发现所有在 NFN 共生中具有特征性作用的豆科植物基因在结瘤物种中都是保守的，只有一个例外。我们观察到大量特定于顺序的基因家族扩展，仅仅因为它们的系统发育分布，可能包括有助于多重增益或后续共生改进的基因。在平行下，我们在 NFN 进化枝内非结瘤物种的 13 个基因组中的 10 个中发现了编码不可或缺的 NFN 共生调节因子 NODULE INCEPTION (NIN) 的基因的多个独立功能丧失事件的特征。该模式表明 NFN 共生至少有 8 个独立的损失。结论 我们发现 NFN 共生的多个独立损失发生在 NFN 进化枝的四个顺序中。这些结果表明 NFN 共生以前比目前更普遍，并且这种共生受到低估的逆向选择压力。系统基因组学和 NFN 共生的进化。结瘤和非结瘤物种的基因组测序与 27 个以前可用的基因组相结合，产生了一个跨越 NFN 进化枝和 NFN 进化枝外物种作为外群的数据集。按照三种系统发育模式识别和过滤正群。这种全基因组分析确定了两个参与 NFN 共生的基因，NIN 和根瘤菌定向极地生长 (RPG)，它们在大多数非结瘤物种中丢失。NFN 共生的多重损失（红十字）的发生表明存在逆向选择压力。植物与固氮细菌的根瘤共生影响全球氮循环和粮食生产，但仅限于开花植物单个进化枝中的一个属子集。为了探索这种分散发生的遗传基础，我们对 10 个植物物种的基因组进行了测序，涵盖了根瘤形态类型、细菌共生体和感染策略的多样性。在对总共 37 个植物物种的全基因组比较分析中，我们在该进化枝内 13 个非结瘤物种基因组中的 10 个中，在不可或缺的共生调节因子 NODULE INCEPTION 中发现了多个独立的功能丧失事件的特征。多个独立的损失塑造了植物中固氮根瘤共生的现代分布的发现揭示了进化历史中系统发育更广泛的分布以及迄今为止被低估的针对这种共生的选择压力。