Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS come from model legumes that exhibit a root-hair mode of bacterial infection in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step towards understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated a comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen scavenging mechanisms in the Papilionoid family. Finally, absence of cysteine-rich motif-1 containing-NCRs, but the recruitment of defensin like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobial symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.

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Symbiotic nitrogen fixation (SNF) inside root-nodules is a primary and sustainable source of soil nitrogen. Understanding nodule development and metabolism in crop legumes may lead to more effective SNF in agriculture. Peanut (Arachis hypogaea) is an economically important allotetraploid legume with non-canonical nodule developmental features. Recent genome sequencing of peanut has opened the possibility of making peanut a model for studying atypical nodule development. To help the community of nodule biologists, we have developed a database called AhNGE (Arachis hypogaea Nodule Developmental Gene Expression: http://nipgr.ac.in/AhNGE/index.php). AhNGE contains RNAseq data from six data points of nodule development in A. hypogagea cv. Tifrunner. This data represents a dynamic view of gene expression during peanut nodule development. Research in model legumes has generated a huge knowledgebase in the last twenty years. To streamline comparative genomics among legumes, we performed ortholog analysis among four legumes (Cicer, Glycine, Lotus, and Medicago) and one non-legume (Arabidopsis). This will facilitate the integration of existing knowledge in nodule development with the Arachis transcriptome. The available data can be retrieved using a single or batch query or searching using gene ID, from above mentioned five species. The output displays the gene expression pattern in graphical as well as tabular form, along with further options to download the sequence data. The database is linked with PeanutBase, the main genomic resource of peanut. Additionally, the expression level of different splicing variants can be retrieved from the database. In summary, AhNGE serves as an important resource for the scientific community working on nodule development.