Long non-coding RNAs (LncRNAs) are one of the many layers of transcription in higher plants. LncRNAs are responsive to biotic and abiotic stresses and regulate genes. In our study, we have identified 905 novel lncRNAs from 8471 drought-responsive, novel transcripts of RNA-Seq reads from two banana cultivars, a drought-tolerant cv. ‘Saba’ (ABB) and -susceptible cv. ‘Grand Naine’ (AAA). Of these 905 lncRNAs, 75 (8.3 %) transcripts were natural antisense RNAs (NATs) and 2 transcripts identified as precursors of microRNA-miR156 and miR166. Among the 905 identified lncRNAs, 216, 150 and 279, 164 lncRNAs were induced and reduced to drought stress, respectively, in tolerant and susceptible in comparison to their equivalent controls. The remaining 22 lncRNA of tolerant cultivars was not regulated by drought stress. Of the 882 drought-responsive lncRNAs, 44 new lncRNAs were identified as induced. Musa lncRNAs were unevenly distributed in 11 chromosomes of Musa acuminata and no lncRNAs were found in chromosome-9 of drought-tolerant cultivar. The average lengths of lncRNAs were 683 nucleotides (nt). Drought-responsive differential expression of lncRNAs was found between +8.11585- and −4.04311-fold. Around 7.9 % of the identified lncRNAs were decoys of 85 conserved microRNAs. These findings will lay a basic platform for effective strategic planning of developing drought-resilient crop varieties.

Soil moisture deficit stress is one of the most important abiotic stresses limiting the production and productivity of banana (Musa spp.). Plant responses to drought stress are regulated at both the transcriptional and post-transcriptional levels. As post-transcriptional gene regulators, microRNAs (miRNAs) regulate gene expression during drought stress. The present study aimed to identify drought-responsive miRNAs in an expressed sequence tag (EST) library of drought-stressed banana and to study their expression in a drought-tolerant banana cultivar, 'Saba', subjected to soil moisture deficit stress. In silico prediction resulted in the identification of three miRNAs (miR156, miR169, and miR2118) whose expression was confirmed using real-time qPCR assays with the respective complementary DNAs (cDNAs) synthesised in multiplex stem-loop-primed reverse-transcription reactions. The selection of a suitable reference miRNA for this study was carried out using six genes, which included the traditional Musa reference gene for 25S rRNA. miR399 was selected as the reference miRNA, based on its constant level of expression in various tissues and sample types. Additional regulatory roles for miR169 on expression of the dehydrin and aquaporin genes in banana were investigated using qPCR assays in drought-stressed leaf samples collected at different times during stress. The results suggested that miR169, miR156, and miR2118 were up-regulated during soil moisture deficit stress, and also that miR169 had an indirect, transcription-level role in regulating dehydrin and aquaporin gene expression. The aquaporin gene exhibited more prominent expression compared to dehydrin in banana during drought stress.