Transcriptomic analysis with the progress of symbiosis in ‘crack-entry’ legume<i>Arachis hypogaea</i>highlights its contrast with ‘infection thread’ adapted legumes

Karmakar, Kanchan; Kundu, Anindya; Rizvi, Ahsan Z.; Dubois, Emeric; Séverac, Dany; Czernic, Pierre; Cartieaux, Fabienne; Dasgupta, Moumita

doi:10.1101/251181

Cited by 5 publications

(7 citation statements)

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“…Transcriptomic analysis is a powerful tool to reveal the interactions between host and pathogen [61][62][63][64]. In this study, we analyzed 35 pairs of samples from 69 pairs of Xooor Mor-infected rice microarray samples deposited in the GEO database.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

2020

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Background: Disease resistance is an important factor that impacts rice production. However, the mechanisms underlying rice disease resistance remain to be elucidated. Results: Here, we show that a robust set of genes has been defined in rice response to the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). We conducted a comprehensive analysis of the available microarray data from a variety of rice samples with inoculation of Xoo and Mor. A set of 12,932 genes was identified to be regulated by Xoo and another set of 2709 Mor-regulated genes was determined. GO enrichment analysis of the regulated genes by Xoo or Mor suggested mitochondrion may be an arena for the up-regulated genes and chloroplast be another for the down-regulated genes by Xoo or Mor. Cytokinin-related processes were most frequently repressed by Xoo, while processes relevant to jasmonic acid and abscisic acid were most frequently activated by Xoo and Mor. Among genes responsive to Xoo and Mor, defense responses and diverse signaling pathways were the most frequently enriched resistance mechanisms. InterPro annotation showed the zinc finger domain family, WRKY proteins, and Myb domain proteins were the most significant transcription factors regulated by Xoo and Mor. KEGG analysis demonstrated pathways including 'phenylpropanoid biosynthesis', 'biosynthesis of antibiotics', 'phenylalanine metabolism', and 'biosynthesis of secondary metabolites' were most frequently triggered by Xoo and Mor, whereas 'circadian rhythmplant' was the most frequent pathway repressed by Xoo and Mor. Conclusions: The genes identified here represent a robust set of genes responsive to the infections of Xoo and Mor, which provides an overview of transcriptional reprogramming during rice defense against Xoo and Mor infections. Our study would be helpful in understanding the mechanisms of rice disease resistance.

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Section: Discussionmentioning

confidence: 99%

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

2020

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“…RNA-seq data are downloaded from https : //www.ncbi.nlm.nih.gov/sra?term = SRP 107173 [6]. These data contain transcriptomic expressions of six root nodule developmental stages after the infection with Bradyrhizobium Semia 6144.…”

Section: Lncrnas Identification and Validationmentioning

confidence: 99%

“…Rhizobia enter through infection thread and root nodule primordium in these plants. As an exception, rhizobia directly invade root cortical cell via epidermal cracks in dalbergoid legumes like Arachis hypogaea [6]. Wild diploids parents of this plant are Arachis duranensis and Arachis ipaensis and their genomes are used for mapping purpose.…”

Section: Introductionmentioning

confidence: 99%

“…Transcriptome data are downloaded for the different stages of symbiosis in A. hypogaea like root invasion stage (1DPI), root nodule primordia formation (4DPI), the spread of infections in the root nodule (8DPI), immature root nodules with rod-shaped rhizobia (12DPI), and mature root nodules with spherical symbiosomes (NOD). Differential gene expression for the progress of symbiosis in A. hypogaea are reported [2] [3] [4] [5] [6] but their epigenetic connections with lncRNAs are explored in this study.…”

Section: Introductionmentioning

confidence: 99%

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Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea

Rizvi

Dhusia

2019

Preprint

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RNA-sequencing (RNA-seq) data analysis of the different stages of root nodules formation in peanut Arachis hypogaea investigate the genetic features. Genes related to the root nodules formations in this plant are extensively studied [1] [2] [3] [4] [5], but less information is present for their relations with long noncoding RNAs (lncRNAs). Bioinformatics techniques are utilised here to identify the novel lncRNAs present in the publically available RNA-seq data reported [6] for the different stages of root nodules formation in this plant. Highly correlated, significant, and Differentially Expressed (DE) gene-lncRNA pairs are also detected to understand the epigenetic control of lncRNA. These pairs are further differentiated between cis and trans antisense lncRNAs and lincRNAs based on their functions and positions from the genes. Obtained results are the catalogue for the highly correlated and significant DE gene-lncRNA pairs related to root nodules formation in A. hypogaea.

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“…Nevertheless, some unresolved questions remain. One of them is that a recent transcriptome analysis in A. hypogaea failed to detect homologs of the Aeschynomene NCR genes ( Karmakar et al, 2018 ). However, this study identified another, small, family of cysteine-containing peptides, related to the antimicrobial PR-1 family and the authors suggested the involvement of these peptides in bacteroid differentiation.…”

Section: Nodule-specific Peptides Targeted To the Symbiosomementioning

confidence: 99%

Impact of Plant Peptides on Symbiotic Nodule Development and Functioning

et al. 2018

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Ribosomally synthesized peptides have wide ranges of functions in plants being, for example, signal molecules, transporters, alkaloids, or antimicrobial agents. Legumes are an unprecedented rich source of peptides, which are used to control the symbiosis of these plants with the nitrogen-fixing Rhizobium bacteria. Here, we discuss the function and the evolution of these peptides playing an important role in the formation or functioning of the symbiotic organs, the root nodules. We distinguish peptides that can be either cell-autonomous or secreted short-range or long-range signals, carrying messages in or between plant cells or that can act as effectors interacting with the symbiotic bacteria. Peptides are further classified according to the stage of the symbiotic process where they act. Several peptide classes, including RALF, DLV, ENOD40, and others, control Rhizobium infection and the initiation of cell divisions and the formation of nodule primordia. CLE and CEP peptides are implicated in systemic and local control of nodule initiation during autoregulation of nodulation and in response to the nutritional demands of the plant. Still other peptides act at later stages of the symbiosis. The PSK peptide is thought to be involved in the suppression of immunity in nodules and the nodule-specific cysteine-rich, GRP, and SNARP (LEED..PEED) peptide families are essential in the functioning of the nitrogen fixing root nodules. The NCRs and possibly also the GRP and SNARPs are targeted to the endosymbionts and play essential roles in the terminal differentiation of these bacteria.

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Transcriptomic analysis with the progress of symbiosis in ‘crack-entry’ legumeArachis hypogaeahighlights its contrast with ‘infection thread’ adapted legumes

Abstract: 27In root-nodule symbiosis, rhizobial invasion and nodule organogenesis are host controlled. In

Cited by 5 publications

References 98 publications

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea

Impact of Plant Peptides on Symbiotic Nodule Development and Functioning

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