Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense

Abstract

BackgroundCavendish, 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.ResultsRNA 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.ConclusionsBoth 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-851) contains supplementary material, which is available to authorized users.

Plant defense response against Fusarium oxysporum and strategies to develop tolerant genotypes in banana

“…Role of JA in banana defense is supported by another study reported by Sun et al (2013) who showed that MeJA treatment dramatically reduced the disease incidence and disease severity of Foc4-infected banana plants compared to control and observed that MeJA treatment has triggered key enzymes of secondary metabolite biosynthetic pathways. Also Li et al (2013a) found that both Foc1 and Foc TR4 infections led to similar gene expression profiles in banana roots where majorly ethylene synthetic genes like ACC oxidase and ethylene signaling pathways were found to be activated. These current studies suggest that banana defense against Foc is signaled mainly by JA and ethylene.…”

“…Using (GFP)-tagged transformants of Foc race 4, Li et al (2011b) have reported that Foc race 4 was capable of invading the epidermal cells of banana roots directly and in banana roots, fungal hyphae were able to penetrate cell walls directly to grow inside and outside cells. In another study, Li et al (2013a) group has monitored the infection process of both GFP-expressing Foc1 (race 1 of Fusarium oxysporum) and Foc TR4 and reported that both were found to be able to invade banana roots and later spread to root vascular tissues.…”

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

“…These encode Fom _ 16257 a Fom -unique protein with unknown function, Fom _ 16301 a SSP encoding a LysM-domain (~40 residue lysin motif implicated in chitin binding [50–52]), and Fom _ 16235 an uncharacterised protein with orthologs in other F. oxysporum ff. spp.. qRT-PCR verification of Fom_16257 expression confirmed increased expression in DZA315 over A17 and absence of expression under in vitro conditions (Fig.…”

Modifying Bananas: From Transgenics to Organics?

“…malaccensis. The genome sequence of M. balbisiana have also been published [53], as well as numerous transcriptomic data from various banana tissues [54][55][56]. In parallel, there are mapping programs to identify loci for various traits, such as resistance to Fusarium wilt TR4.…”