Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical
race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world.
The disease can be managed in the field by planting resistant Cavendish plants generated by
somaclonal variation. However, little information is available on the genetic basis of plant
resistance to Foc TR4. To a better understand the defense response of resistant banana plants
to the Fusarium wilt pathogen, the transcriptome profiles in roots of resistant and susceptible
Cavendish banana challenged with Foc TR4 were compared.
RNA-seq analysis generated more than 103 million 90-bp clean pair end (PE) reads, which
were assembled into 88,161 unigenes (mean size = 554 bp). Based on sequence similarity
searches, 61,706 (69.99%) genes were identified, among which 21,273 and 50,410 unigenes
were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG),
respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database
(KEGG) mapped 33,243 (37.71%) unigenes to 119 KEGG pathways. A total of 5,008 genes
were assigned to plant-pathogen interactions, including disease defense and signal
transduction. Digital gene expression (DGE) analysis revealed large differences in the
transcriptome profiles of the Foc TR4-resistant somaclonal variant and its susceptible wildtype.
Expression patterns of genes involved in pathogen-associated molecular pattern
(PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and
biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors,
signaling/regulatory genes, cell wall modification genes and genes with other functions were
analyzed and compared. The results indicated that basal defense mechanisms are involved in
the recognition of PAMPs, and that high levels of defense-related transcripts may contribute
to Foc TR4 resistance in banana