Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection

Abstract

Dry root rot (Rhizoctonia bataticola) is an important disease of lentils (Lens culinaris Medik.).To gain an insight into the molecular aspects of host-pathogen interactions, the RNA-seq approach was used in lentils following inoculation with R.bataticola. The RNA-Seq has generated >450 million high-quality reads (HQRs) and nearly 96.97% were properly aligned to the reference genome. Very high similarity in FPKM (fragments per kilobase of exon per million mapped fragments) values (R > 0.9) among biological replicates showed the consistency of the RNA-Seq results. The study revealed various DEGs (differentially expressed genes) that were associated with changes in phenolic compounds, transcription factors (TFs), antioxidants, receptor kinases, hormone signals which corresponded to the cell wall modification enzymes, defense-related metabolites, and jasmonic acid (JA)/ethylene (ET) pathways. Gene ontology (GO) categorization also showed similar kinds of significantly enriched similar GO terms. Interestingly, of the total unigenes (42,606), 12,648 got assembled and showed significant hit with Rhizoctonia species. String analysis also revealed the role of various disease responsive proteins viz., LRR family proteins, LRR-RLKs, protein kinases, etc. in the host-pathogen interaction. Insilico validation analysis was performed using Genevestigator® and DEGs belonging to six major defense-response groups viz., defense-related enzymes, disease responsive genes, hormones, kinases, PR (pathogenesis related) proteins, and TFs were validated. For the first time some key miRNA targets viz. miR156, miR159, miR167, miR169, and miR482 were identified from the studied transcriptome, which may have some vital role in Rhizoctonia-based responses in lentils. The study has revealed the molecular mechanisms of the lentil/R.bataticola interactions and also provided a theoretical approach for the development of lentil genotypes resistant to R.bataticola.

Unraveling the pathways influencing the berry color and firmness of grapevine cv. Flame Seedless treated with bioregulators using biochemical and RNA-Seq analysis under semi-arid subtropics

“…This study could validate 19 genes using Genevestigator, and similar interpretations were also made by Mishra et al (2021) while studying the gene co-expression analysis for disease gene prediction. Additionally, Guo et al (2019) used qRT-PCR to confirm the accuracy and consistency of the transcriptome analysis results, finding that chosen genes had similar expression levels in treated and control grape berries.…”

Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.)

“…These novel markers can be used for the identification of linked markers using some mapping population for its application in the marker-assisted selection for seed size traits in lentils ( Bosamia et al, 2015 ). Micro-RNAs (miRNAs) are the class of small noncoding RNAs (∼21-nucleotide long) that control the post-transcriptional expression of mRNA in lentils ( Mishra et al, 2022 ). The miRNAs interact with the target mRNAs after getting loaded into the Ago-proteins ( Dueck et al, 2012 ) and thus prevent gene expression ( Winter et al, 2009 ).…”

Morphological, Molecular, and Biochemical Characterization of a Unique Lentil (Lens culinaris Medik.) Genotype Showing Seed-Coat Color Anomalies Due to Altered Anthocyanin Pathway

“…(DPPH scavenging activity (%) = Abs Control -Abs Sample /(Abs Control ) × 100 , (1) where, Abs Control is the absorbance of DPPH radical + methanol, and Abs Sample is the absorbance of DPPH radical + sample extract.…”

“…Lentil is an important cool-season legume crop of India and is cultivated mainly as a rainfed crop [ 1 ]. Globally, it is cultivated in an area of 4.8 million ha and yields 5.73 Mt [ 2 ].…”