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Background  Walnut anthracnose induced by  Colletotrichum gloeosporioides  is a disastrous disease affecting walnut production. The resistance of walnut fruit to  C. gloeosporioides  is a highly complicated and genetically programmed process. However, the underlying mechanisms have not yet been elucidated.    Results  To understand the molecular mechanism underlying the defense of walnut to  C. gloeosporioides , we used RNA sequencing and label-free quantitation technologies to generate transcriptomic and proteomic profiles of tissues at various lifestyle transitions of  C. gloeosporioides , including 0 hpi, pathological tissues at 24 hpi, 48 hpi, and 72 hpi, and distal uninoculated tissues at 120 hpi, in anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts, which were defined through scanning electron microscopy. A total of 21,798 differentially expressed genes (DEGs) and 1929 differentially expressed proteins (DEPs) were identified in F26 vs. F423 at five time points, and the numbers of DEGs and DEPs were significantly higher in the early infection stage. Using pairwise comparisons and weighted gene co-expression network analysis of the transcriptome, we identified two modules significantly related to disease resistance and nine hub genes in the transcription expression gene networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the DEGs and DEPs revealed that many genes were mainly related to immune response, plant hormone signal transduction, and secondary metabolites, and many DEPs were involved in carbon metabolism and photosynthesis. Correlation analysis between the transcriptome data and proteome data also showed that the consistency of the differential expression of the mRNA and corresponding proteins was relatively higher in the early stage of infection.    Conclusions  Collectively, these results help elucidate the molecular response of walnut fruit to  C. gloeosporioides  and provide a basis for the genetic improvement of walnut disease resistance.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03042-1.

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides