The Comprehensive Detection of mRNAs, lncRNAs, circRNAs, and miRNAs in Lychee Response to Lychee Downy Blight

Lychee downy blight (LDB) is an oomycete pathogen (Peronophythora litchi) disease, which affects the fruits and leaves of lychee, resulting in economic losses. Chemical fungicides are commonly used for disease control, while for eco-safety measures, the study of molecular mechanisms involved in lychee resistance against LDB is necessary. Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular (circRNAs), and microRNAs (miRNAs), play a crucial role in plant disease resistance. To examine lychee response (fruits and leaves) to LDB, we studied the expression patterns of ncRNAs and mRNAs under LDB treatment. By whole transcriptome sequencing analyses, a total of 36,885 mRNAs, 2627 lncRNAs, 4682 circRNAs, and 525 miRNAs were identified in lychee. A differential expression (DE) analysis revealed that there were 1095 DEmRNAs, 89 DElncRNAs, 28 DEcircRNAs, and 28 DEmiRNAs in the LDB-treated fruits, as well as 1158 DEmRNAs, 132 DElncRNAs, 13 DEcircRNAs, and 197 DEmiRNAs in the LDB-treated leaves. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the potential function of DEmRNAs and the targets of ncRNAs were involved in plant defense. Furthermore, co-expression networks of putative interacting ncRNAs and mRNAs were developed, in which mRNAs encoded some receptor proteins, pointing to potential ncRNAs associated with LDB infection. Our study provided a new, brief insight to the putative role of ncRNAs in lychee response to LDB.