Genome-wide identification of novel, long non-coding RNAs responsive to Mycosphaerella eumusae and Pratylenchus coffeae infections and their differential expression patterns in disease-resistant and sensitive banana cultivars

Abstract

Long non-coding RNAs (lncRNAs) are important regulators of gene expression in plant response to biotic and abiotic stresses. The participation of lncRNAs in plant disease resistance in bananas is largely unknown. Therefore, we attempted to identify novel lncRNAs responsive to Mycosphaerella eumusae, a causative agent of Eumusae leaf spot disease and root lesion nematode, Pratylenchus coffeae and their differential expression patterns during stress and normal conditions in respective resistant and sensitive banana genotypes. Illumina paired-end transcriptome sequencing of control and infected samples of resistant and sensitive banana cultivars was performed and the sequence reads assembled into 172434, 201256 transcriptional units (TUs) for M. eumusae and P. coffeae, respectively. The genome-wide analysis for ELSD-responsive lncRNAs led to identification of 5142 novel lncRNAs including 3031-intergenic, 1672-intragenic, and 440 antisense lncRNAs classes collectively from ELSD-resistant and sensitive cultivars. Similarly, 5615 lncRNAs comprised of 3283 intergenic, 1878-intragenic, and 454 antisense classes were identified from P. coffeae-infected resistant and sensitive banana cultivars. Most of the lncRNAs were stress specific, evenly distributed among banana chromosomes and the average length is ranging from 620 to 684 nucleotides. In addition, 1250 and 1284 lncRNAs were differentially expressed to M. eumusae and P. coffeae infections, respectively. The LncRNA–mRNA interaction-based functional role showed lncRNA-mediated downregulation of horcolin, an antifungal protein is likely responsible for ELSD sensitivity in banana cultivars. Furthermore, we identified 100 of these lncRNAs also play a role in drought stress response of banana indicating a possible crosstalk between biotic and abiotic stresses.