title: Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum.
abstract: Penicillium expansum is a destructive phytopathogen that causes decay in deciduous fruits during postharvest handling and storage. During colonization the fungus secretes D-gluconic acid (GLA), which modulates environmental pH and regulates mycotoxin accumulation in colonized tissue. Till now no transcriptomic analysis has addressed the specific contribution of the pathogen's pH regulation to the P. expansum colonization process. For this purpose total RNA from the leading edge of P. expansum-colonized apple tissue of cv. 'Golden Delicious' and from fungal cultures grown under pH 4 or 7 were sequenced and their gene expression patterns were compared.
  
  
  
  We present a large-scale analysis of the transcriptome data of P. expansum and apple response to fungal colonization. The fungal analysis revealed nine different clusters of gene expression patterns that were divided among three major groups in which the colonized tissue showed, respectively: (i) differing transcript expression patterns between mycelial growth at pH 4 and pH 7; (ii) similar transcript expression patterns of mycelial growth at pH 4; and (iii) similar transcript expression patterns of mycelial growth at pH 7. Each group was functionally characterized in order to decipher genes that are important for pH regulation and also for colonization of apple fruits by Penicillium. Furthermore, comparison of gene expression of healthy apple tissue with that of colonized tissue showed that differentially expressed genes revealed up-regulation of the jasmonic acid and mevalonate pathways, and also down-regulation of the glycogen and starch biosynthesis pathways.
  
  
  
  Overall, we identified important genes and functionalities of P. expansum that were controlled by the environmental pH. Differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions (pH, in vitro or in vivo) to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Comparison between the activation of the colonized host's gene responses by alkalizing Colletotrichum gloeosporioides and acidifying P. expansum pathogens indicated similar gene response patterns, but stronger responses to P. expansum, suggesting the importance of acidification by P. expansum as a factor in its increased aggressiveness.
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.|Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel.
authors.forename: Shiri
authors.initials: S
authors.lastname: Barad
authors.affiliation: Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan, 50250, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Sela
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.
authors.forename: Dilip
authors.initials: D
authors.lastname: Kumar
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.
authors.forename: Amit
authors.initials: A
authors.lastname: Kumar-Dubey
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel.|Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel.
authors.forename: Nofar
authors.initials: N
authors.lastname: Glam-Matana
authors.affiliation: Genomics Unit, ARO, the Volcani Center, Bet Dagan, 50250, Israel.
authors.forename: Amir
authors.initials: A
authors.lastname: Sherman
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel. dovprusk@volcani.agri.gov.il.
authors.forename: Dov
authors.initials: D
authors.lastname: Prusky
mesh_terms: D005656:Fungal Proteins / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006863:Hydrogen-Ion Concentration; D027845:Malus / Q000235:genetics / Q000382:microbiology*; D005810:Multigene Family; D010407:Penicillium / Q000235:genetics / Q000254:growth & development*; D010940:Plant Proteins / Q000235:genetics*; D025341:Principal Component Analysis; D017423:Sequence Analysis, RNA
chemical_list: D005656:Fungal Proteins; D010940:Plant Proteins
keywords: Apple genes regulated by pH; Fungal genes regulated by pH; Gene expression; Pathogenicity; Penicillium expansum; RNA-seq; Transcription profiling; pH regulation; pH-regulated genes