Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness. Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants. Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.

中文翻译：

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植物转录组分析揭示了苜蓿及其低于物种水平的根瘤菌共生体之间的特定分子相互作用。

豆科植物响应其共生的根瘤菌对共生定居和感染的反应而改变基因表达的模式，但是很少在物种水平以下检查转录组反应的程度。在这里，我们描述了12种苜蓿根瘤菌的鉴定，它们在苜蓿（Medicago sativa L.）的根中形成固氮结节，然后对四个苜蓿品种分别接种了两个苜蓿大肠杆菌进行了比较RNA-seq分析。菌株的共生性能和系统发育相关性各不相同。根瘤菌的生物型是根据它们的共生性能，特别是枝干重确定的。通过比较RNA-seq数据与未接种对照植物的RNA-seq数据，确定差异表达基因（DEGs）和代谢途径。比较发现，接种两个根瘤菌菌株后，每个品种产生的DEG之间存在显着差异（P <0.01）。总共表达了8111个基因，约占苜蓿分支杆菌基因组的17.1％。每种苜蓿品种的DEGs比例为0.5％至12.2％。有趣的是，在黄酮类生物合成和植物-病原体相互作用（NBS-LRR）中具有预测作用的基因被确定为最重要的DEG。其他DEG包括Medsa002106和编码结节蛋白和NCR肽的基因，其表达在固氮结节形成过程中被特异性诱导。更重要的是，在植物转录组（DEG和KEGG途径）与两种根瘤菌接种物之间的系统发生距离之间观察到强烈的显着正相关。苜蓿在以下物种水平下（即生物型或菌株）响应不同根瘤菌菌株的感染而表达出明显不同的基因集。特定相互作用基础的候选基因包括Medsa002106以及编码NBS-LRR家族中的结节蛋白，NCR肽和蛋白质的那些。