Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.固氮根瘤菌（nitrogen-fixing rhizobia）寄生形成根瘤是豆科植物（legumes）的经典特征，但其他植物类群亦可形成根瘤，其共生微生物可为根瘤菌或放线菌弗兰克氏菌（actinomycete Frankia）。学界普遍认为结瘤作用（nodulation）曾多次独立演化，但该假说始终缺乏分子遗传学证据支撑——根瘤演化背后的核心遗传改变机制仍不明晰。本研究以仅有的可与根瘤菌建立固氮根瘤的非豆科植物——寄生木属（Parasponia，大麻科Cannabaceae）物种为材料，开展遗传学与比较基因组学（comparative genomics）研究。通过安德森寄生木（Parasponia andersonii）与其不结瘤近缘物种毛叶山黄麻（Trema tomentosa）的属间杂交（intergeneric crosses）实验，证实结瘤器官发生（nodule organogenesis）为显性遗传性状，而胞内侵染（intracellular infection）并非该类群的显性性状。对安德森寄生木与豆科植物蒺藜苜蓿（Medicago truncatula）的比较转录组学（comparative transcriptomics）分析显示，二者根瘤组织中共利用至少290个同源共生基因（orthologous symbiosis genes），其中包含豆科植物中结瘤过程必需的关键基因，如结瘤起始基因（NODULE INCEPTION, NIN）与根瘤菌定向极性生长基因（RHIZOBIUM-DIRECTED POLAR GROWTH, RPG）。对3种寄生木属物种及相关不结瘤植物物种的基因组比较分析表明，不结瘤类群中存在结瘤因子感知基因（NOD FACTOR PERCEPTION）、NIN与RPG的推定同源基因平行丢失（parallel loss）的现象，这类共生核心基因的平行丢失提示这些不结瘤植物类群已彻底丧失了结瘤潜能。综上，本研究结果对“结瘤作用多次独立演化”的主流观点提出了挑战，并提出新的演化假说：结瘤作用可能于约1亿年前在所有结瘤植物的共同祖先中起源，随后在众多后裔类群中独立丢失，这一结论将为旨在作物中工程化构建固氮根瘤的转化研究手段（translational approaches）带来深远影响。