Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation

Abstract

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.

Nodule INception‐independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea)

“…Rhizobia were present in most of the cells where the auxin response was active. After endocytosis, the bacteroids continue to have a small, elongated shape (E‐type), which eventually are converted to a spherical shape (Sinharoy & DasGupta, 2009; Raul et al ., 2022). Interestingly, the nuclear auxin response was present only in those cells where the bacteroids are of E‐type (Fig.…”

“…RNA sequencing (RNAseq) profiling of different stages of nodule development revealed that the transcriptomic signature in peanut is both conserved as well as diversified in different modules compared to model legumes (Raul et al ., 2022). In the present study, using promoter‐aided reporter analysis and RNA in situ hybridization (ISH), we show that spatial expression of NIN is restricted to the root pericycle and inner cortical layers during nodule primordia initiation.…”

Molecular Mechanisms of Intercellular Rhizobial Infection: Novel Findings of an Ancient Process

“…In A. hypogeae , known symbiotic genes acting in the common IT mediated nodulation (125 peanut orthologs) are also expressed during symbiosis ( Figure 2 ). The majority of DEGs are observed during nodule functioning, then nodule organogenesis and finally infection ( Raul et al, 2022 ). Transcriptomic analyses of a time-course experiment in A. evenia allowed the identification of DEGs at early and late stages of the symbiotic interaction.…”

Fine-Tuned Immune Antagonism and Nodule-Specific Cysteine-Rich Peptides Govern the Symbiotic Specificity Between Alfalfa Cultivars and Ensifer meliloti

“…Some immune response-activated genes, namely TIR-NBS-LRR, LRR-RLK, EF-hand pair protein, and WAKL (Kumar et al 2020), were also induced excessively in G9 plants compared with G3 plants. Despite the slight induction of defense response-related genes, namely FLS2, (Liu et al 2017), in G9 plants, as well as the marginally suppressed disease resistance proteins, namely RPM1 (NBS-LRR, LRR, and NB-ARC) and RPS2, in G3 plants, both defense-related gene induction (i.e., PR1) and the E. meliloti secretion system, which triggers the ETI process (i.e., HSP90), were induced to a larger extent in G3 plants, indicating an enhanced control of rhizobial proliferation and an elevated defense/resistance of G3 plants to bacteroids (Li et al 2020a, b;Raul et al 2021). The ubiquitin proteasome system (UPS) induces, regulates, and terminates plant responses to stress, and E3 ubiquitin ligase can positively regulate plant tolerance to biological stress (Li et al 2020a, b).…”