Ressive reduction in the amount of fungus present at later time points in the incompatible interaction (data not shown). Di Pietro and colleagues [2] found that, having reached the xylem, the fungus remains exclusively within the vessels using them to colonize the host rapidly, mainly through the production order JNJ-26481585 28914615″ title=View Abstract(s)”>PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 of microconidia rather than mycelia which, in turn, progressively grows inside the xylem inducing vessel clogging. In contrast to this prominent microconidia model [20,23], studies using GFPlabeled F. oxysporum have shown that neither conidiophores nor microconidia are found in Arabidopsis or tomato xylem [21,22]. The response to infection may be affected by inoculum concentration, the age of the plant, the duration of exposure to the inoculum, and the type of substrate for plant growth (e. g. sand or soil) [11,27]. The assessment time points may also play an important role in the picture that emerges of the host/pathogen genetic responses. Nevertheless, differences in the infection process are likely to occur among different formae speciales and between different experimental designs.Genetic elements of host colonization and pathogenicityMost transcriptomics studies involving F. oxysporum have focused on the interactions that occur in the xylem, and these studies suggest that the main resistance responses occur within or along the vessels. In this context, genes that are expressed solely in planta and not in artificial culture are the most interesting because they are likely virulence factors (Table 2 and Additional File 2). We identified 195 genes that were expressed in planta, 72 of which ( 37 ) were not expressed under artificial culture conditions and therefore represent putative virulence factors. Interestingly, only 11 out of 218 genes in cotton plants infected with F. oxysporum f. sp. vasinfectum were expressed specifically in planta [50]. The group of putative virulence factors identified in our analysis included plant cell wall degrading enzymes (CWDEs), represented by five transcripts encoding pectate lyases, endo-1,4 beta xylanases and endo-1,4 beta glucanases, possibly activated by interaction with the host. Among these transcripts, an endo-1,4-beta-xylanase 2 precursor is the only sequence peculiar to race 1, induced in the incompatible interaction, while the other four TDFs are specific to the race 1,2 strains. Like most fungi, F. oxysporum secretes CWDEs during either penetration or colonization [23]. Although the inactivation of individual CWDE- or protease-encoding genes might not have a detectable impact on virulence (reviewed in [2]), possibly because of functional redundancy, their activity is crucial in the process of fungal colonization. Active fungal growth isTable 4 Real time RT-PCR expression analysis of selected Fusarium oxysporum f. sp. melonis (FOM) genesID P493 P135 P1315 P819 P1403 Homology FOXT_12671 FOXT_08523 FOXG_05190 FOXG_09125 FOXT_13204 E-value 5E-152 1E-48 2E-79 2E-117 7E-51 Annotation Fusarium oxysporum f.sp lycopersici aspartate aminotransferase Fusarium oxysporum f.sp lycopersici acyl-CoA desaturase Fusarium oxysporum f.sp lycopersici E3 ubiquitin-protein ligase Fusarium oxysporum f.sp lycopersici hypothetical protein similar to avenacinase Fusarium oxysporum f.sp lycopersici predicted protein Ct 3.43 16.11 3.99 10.24 7.06 SD 0.11 0.41 0.31 0.04 0.Five Fusarium oxysporum f. sp. melonis transcripts, expressed in planta during infection according to cDNA-AFLP experiments, were selected for val.