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

Gyan P Mishra,Ranjeet Ranjan Kumar,Dwijesh Chandra Mishra,Shiv Kumar,Jyoti Devi,Harsh Kumar Dikshit,Tejas Bosamia,Kuldeep Tripathi,Shiksha Chaurasia,Manju Kohli,Muraleedhar S Aski,Shaily Javeria,Jyotika Bhati,Amit Kumar Singh,Atul Kumar

doi:10.3390/genes13010090

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.

Highlights

Lentil (L. culinaris Medik.) is an important edible legume and annual self-pollinating crop with an average genome size of 4 Gbp [1,2]
The RNA was extracted from the root tissues of L. culinaris plants from both the control and the infected (R. bataticola -inoculated) plants and transcriptional changes were analyzed during fungus infection over the control using Illumina Hiseq
The RNA-Seq analysis has conclusively shown that the R. bataticola infection in lentils triggers the expression of a complex gene network which helps in the establishment of fungal growth in the roots of lentil plant

Summary

Introduction

Lentil (L. culinaris Medik.) is an important edible legume and annual self-pollinating crop with an average genome size of 4 Gbp [1,2]. Lentil which is known as red dhal or Masur provides an inexpensive source of nutrition including carbohydrates, proteins, dietary fibers, vitamins, and micronutrients to a large section of the poor population that are residing in developing countries [3,4,5,6]. Lentil is a rich source of non-nutritional components such as tannins and phytic acid which plays a key role in imparting defense against fungus, insects, and parasites [7,8]. 5.73 million tons (from 4.8 m ha) in 2019 with Canada being the largest producer (2.17 mt from 1.49 m ha), followed by India (1.23 mt from 1.36 mha), and Australia

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