BACKGROUND: Cavendish, the most widely grown banana cultivar, is relatively 
resistant to Race 1 of Fusarium oxysporum f. sp. cubense (Foc1) which caused 
widespread Panama disease during the first half of the 20th century but is 
susceptible to Tropical Race 4 of Foc (Foc TR4) which is threatening world 
banana production. The genome of the diploid species Musa acuminata which is the 
ancestor of a majority of triploid banana cultivars has recently been sequenced. 
Availability of banana transcriptomes will be highly useful for improving banana 
genome annotation and for biological research. The knowledge of global gene 
expression patterns influenced by infection of different Foc races will help to 
understand the host responses to the infection.
RESULTS: RNA samples from different organs of the Cavendish cultivar were pooled 
for deep sequencing using the Illumina technology. Analysis of the banana 
transcriptome led to identification of over 842 genes that were not annotated by 
the Musa genome project. A large number of simple nucleotide polymorphisms 
(SNPs) and short insertions and deletion (indels) were identified from the 
transcriptome data. GFP-expressing Foc1 and Foc TR4 were used to monitor the 
infection process. Both Foc1 and Foc TR4 were found to be able to invade banana 
roots and spread to root vascular tissues in the first two days following 
inoculation. Digital gene expression (DGE) profiling analysis reveal that the 
infection by Foc1 and Foc TR4 caused very similar changes in the global gene 
expression profiles in the banana roots during the first two days of infection. 
The Foc infection led to induction of many well-known defense-related genes. Two 
genes encoding the ethylene biosynthetic enzyme ACC oxidase and several 
ethylene-responsive transcription factors (ERF) were among the strongly induced 
genes by both Foc1 and Foc TR4.
CONCLUSIONS: Both Foc1 and Foc TR4 are able to spread into the vascular system 
of banana roots during the early infection process and their infection led to 
similar gene expression profiles in banana roots. The transcriptome profiling 
analysis indicates that the ethylene synthetic and signalling pathways were 
activated in response to the Foc infection.