Journal Article

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

Wang, Xiaohua, Lu, Xiaofei, Dai, Shengjie, Yuan, Mei, Liu, Zhenning, Zhao, Ge, Li, Hui, Xu, Ping, Cui, Xiaoyu

2022

Overview

Background Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown. Results The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes. Conclusion The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Animals / Arachis - genetics / Arachis - parasitology / Biological activity / Biomedical and Life Sciences / Competing endogenous RNA / Corn / Crop diseases / Crop rotation / Diseases and pests / Essential oils / Flavonoids / Gene expression / Genetic aspects / Genomes / Genomics / Growth / Insecticides / Legumes / Life Sciences / Methods / Microarrays / Microbial Genetics and Genomics / MicroRNAs - genetics / miRNA / Molecular mechanics / Molecular mechanism / Nematoda - pathogenicity / Nematodes / Non-coding RNA / Nutrient content / Nuts / Oxidation / Peanut / Peanuts / Peroxidase / Plant diseases / Plant Diseases - genetics / Plant Diseases - parasitology / Plant Genetics and Genomics / Plant resistance / Prevention / Proteomics / Reduction / Regulatory network / Ribonucleic acid / Ribonucleotides / Risk factors / RNA / RNA, Circular - genetics / RNA, Long Noncoding - genetics / RNA, Messenger - genetics / Root-knot / Root-knot nematode / Roots / Synthesis / Tomatoes / Transcriptomes / Variance analysis / Xylem