A large part of transcripts is non-coding, which is transcribed from junk DNA; long non-coding RNAs and micro-RNAs regulate the expression levels of mRNAs. For the first time, we identified lncRNAs and miRNAs with their regulatory role in the disease tolerance of Theobroma cacao. In this study, about 2616 lncRNAs and 153 miRNAs were identified from 10 RNA-seq data representing healthy and witches’ broom diseased tissues of cocoa. Around 604 lncRNAs are differentially expressed among healthy and diseased tissues. LncRNAs targeted 9692 mRNAs; 8827 are cis-acting, and 765 are trans-acting. Among targeted mRNAs, 281 are disease resistance-related transcripts, and 211 Transcription Factors (TFs) belong to more than 50 TF families, which were found to be involved in the regulation of the disease tolerance process. The identified 153 miRNAs belong to 27 miR families, and around 5337 mRNAs are targeted by the miRNAs, among them 114 code for TFs and 170 code for disease resistance protein. Ethylene responsive factor, bHLH, WRKY, MYB, bZIP, GTE, GATA, and Heat stress transcription factors are the dominant TFs targeted by lncRNAs, and miRNAs play vital roles in disease progression and tolerance. A total of 55 lncRNAs-miRNAs interacting pair is identified, which were working on endogenous target mimics (e-TMs) mechanism and influenced the expression of 955 mRNAs. The Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) biological pathway analysis reveal that ncRNAs and their targets mRNAs code for transcription factors, and genes that are involved in the disease tolerance processes, including synthesis of disease resistance proteins, amino acids, antibiotics, intracellular proteins that directly or indirectly recognize pathogen effectors are essential for plant biotic stress condition. Our study provides lncRNA and miRNA-based regulatory insight into the genes governing disease progression and tolerance in cocoa.

Keywords: Long non-coding RNA, micro-RNA, miRNAs-lncRNAs interaction, Theobroma cacao L.