Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis

Background: Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations. Results: Melon plants (cv. Charentais Fom-2), which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi), and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi) to obvious wilting symptoms (21 dpi) were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs) differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races/strains. Conclusion: Our data suggest that resistance against FOM in melon involves only limited transcriptional changes, and that wilting symptoms could derive, at least partially, from an active plant response. We discuss the pathogen-derived transcripts expressed in planta during the infection process and potentially related to virulence functions, as well as transcripts that are differentially expressed between the two FOM races grown in vitro. These transcripts provide candidate sequences that can be further tested for their ability to distinguish between races. Sequence data from this article have been deposited in GenBank, Accession Numbers: HO867279-HO867981

Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin

Background: Grapevine berry, a nonclimacteric fruit, has three developmental stages; the last one is when berrycolor and sugar increase. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of thisripening stage. The transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the late stages ofripening between 22 and 37 \ub0Brix was assessed using whole-genome micorarrays.Results: The transcript abundance of approximately 18,000 genes changed with \ub0Brix and tissue type. There were alarge number of changes in many gene ontology (GO) categories involving metabolism, signaling and abioticstress. GO categories reflecting tissue differences were overrepresented in photosynthesis, isoprenoid metabolismand pigment biosynthesis. Detailed analysis of the interaction of the skin and pulp with \ub0Brix revealed that therewere statistically significantly higher abundances of transcripts changing with \ub0Brix in the skin that were involved inethylene signaling, isoprenoid and fatty acid metabolism. Many transcripts were peaking around known optimalfruit stages for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF superfamilyof transcription factors changed during these developmental stages. The transcript abundance of a unique clade ofERF6-type transcription factors had the largest changes in the skin and clustered with genes involved in ethylene,senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcriptabundance of important transcription factors involved in fruit ripening was also higher in the skin.Conclusions: A detailed analysis of the transcriptome dynamics during late stages of ripening of grapevine berriesrevealed that these berries went through massive transcriptional changes in gene ontology categories involvingchemical signaling and metabolism in both the pulp and skin, particularly in the skin. Changes in the transcriptabundance of genes involved in the ethylene signaling pathway of this nonclimacteric fruit were statisticallysignificant in the late stages of ripening when the production of transcripts for important flavor and aroma compoundswere at their highest. Ethylene transcription factors known to play a role in leaf senescence also appear to play a role infruit senescence. Ethylene may play a bigger role than previously thought in this non-climacteric fruit