Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus.

Long non-coding RNAs (lncRNAs) serve as crucial regulators in plant response to various diseases, while none have been systematically identified and characterized in response to citrus Huanglongbing (HLB) caused by Liberibacter asiaticus (Las) bacteria. Here, we comprehensively investigated the transcriptional and regulatory dynamics of the lncRNAs in response to L. Samples were collected from leaf midribs of Las- and mock-inoculated HLB-tolerant rough lemon () and HLB-sensitive sweet orange () at week 0, 7, 17, and 34 following inoculation using Las+ budwood of three biological replicates in the greenhouse. A total of 8,742 lncRNAs, including 2,529 novel lncRNAs, were identified from RNA-seq data with rRNA-removed from strand-specific libraries. Genomic variation analyses of conserved lncRNAs from 38 citrus accessions showed that 26 single nucleotide polymorphisms (SNPs) were significantly correlated with HLB. In addition, lncRNA-mRNA weighted gene co-expression network analysis (WGCNA) showed a significant module correlated with Las-inoculation in rough lemon. Notably, the most significant and multiple co-expressed genes related to plant defense in the module were targeted by , suggesting that might compete with endogenous to maintain the homeostasis of immune gene expression levels. Candidate and genes targeted by were identified as two key hub genes interacting with bacteria pathogen response genes based on the prediction of protein-protein interaction (PPI) network. These two genes were also found within HLB-associated QTL in linkage group 6. Overall, our findings provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation.