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Genome-wide identification of lncRNAs, miRNAs, mRNAs, and their regulatory networks involved in tapping panel dryness in rubber tree (Hevea brasiliensis).

Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis) is largely unknown. Here, the whole transcriptomes of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNA (DEMs), genes (DEGs), and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs, and 1,574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. KEGG analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were down-regulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and two and 44 DELs were predicted as precursors and endogenous target mimics (eTMs) of two and six DEMs, respectively. Based on these, the DEL-DEM-DEG regulatory network involved in TPD was constructed, and 13 hub DELs, three hub DEMs and two hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of lncRNAs, miRNAs, and genes involved in TPD in rubber tree.