Identification of Mycosphaerella eumusae responsive unique genes / transcripts from a resistant banana cultivar.

Abstract

Next generation sequencing was performed using an Illumina Hiseq platform in leaf cDNA libraries of unchallenged and Mycosphaerella eumusae challenged plants of banana cultivars with contrasting reactions to the leaf fungus, resistant ‘Manoranjitham’ (AAA genome, unique) and susceptible ‘Grand Naine’ (AAA genome, Cavendish subgroup). Thirty-six million reads obtained from each library were assembled with the Musa acuminata genome sequence as a reference, using TOPHAT2 and Cufflinks software. Approximately 45,000 unigenes were obtained from each library and annotated against Musa and Viridae plantae databases. A comparison of the expression pattern from these four libraries was made based on digital gene expression (DGE) profiles. Major transitional shifts in gene expression were noticed among these four libraries. It was observed that nearly 4658 and 3261 transcripts were over-expressed in challenged libraries of the resistant and susceptible cultivar, respectively. Interestingly, the number of over-expressed transcripts was higher in the challenged resistant cultivar than in the challenged susceptible one. A total of 46 and 8 unique transcripts, which were significantly over- and under-expressed, respectively, in the challenged resistant cultivar, were identified. The M. eumusaechallenged resistant cultivar exhibited 36 pathogenesis-related gene families and 10 transcription factors. These findings are expected to lead towards the identification of candidate genes responsible for M. eumusae resistance in banana. This study revealed that pathogen resistance mechanisms in banana are part of a complex network of defense mechanisms through signal transduction involving ROS, lignin biosynthesis, hormonal pathways, detoxification and production of secondary metabolites. Apart from helping to elucidate resistance mechanisms, the transcriptome data are also being used for identifying functional markers for further use in breeding programs for pathogen resistance.