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Background  Postharvest losses of citrus fruit due to green mold decay, caused by the fungus  Penicillium digitaum , have a considerable economic impact. However, little is known about the molecular processes underlying the response of citrus fruit to  P. digitatum .    Results  Here we describe the construction of a subtracted cDNA library enriched in citrus genes preferentially expressed in response to pathogen infection followed by cDNA macroarray hybridization to investigate gene expression during the early stages of colonization of the fruit's peel by  P. digitatum . Sequence annotation of clones from the subtracted cDNA library revealed that induction of secondary and amino acid metabolisms constitutes the major response of citrus fruits to  P. digitatum  infection. Macroarray hybridization analysis was conducted with RNA from either control, wounded, ethylene treated or  P. digitatum  infected fruit. Results indicate an extensive overlap in the response triggered by the three treatments, but also demonstrated specific patterns of gene expression in response to each stimulus. Collectively our data indicate a significant presence of isoprenoid, alkaloid and phenylpropanoid biosynthetic genes in the transcriptomic response of citrus fruits to  P. digitatum  infection. About half of the genes that are up-regulated in response to pathogen infection are also induced by ethylene, but many examples of ethylene-independent gene regulation were also found. Two notable examples of this regulation pattern are the genes showing homology to a caffeine synthase and a berberine bridge enzyme, two proteins involved in alkaloid biosynthesis, which are among the most induced genes upon  P. digitatum  infection but are not responsive to ethylene.    Conclusions  This study provided the first global picture of the gene expression changes in citrus fruit in response to  P. digitatum  infection, emphasizing differences and commonalities with those triggered by wounding or exogenous ethylene treatment. Interpretation of the differentially expressed genes revealed that metabolism is redirected to the synthesis of isoprenes, alkaloids and phenylpropanoids.

A transcriptomic approach highlights induction of secondary metabolism in citrus fruit in response to Penicillium digitatum infection