Genome sequence and spore germination associated transcriptome analysis of Corynespora cassiicola from cucumber

Abstract Corynespora cassiicola as a necrotrophic plant pathogenic ascomycetes fungus can infect hundreds of species of plants, and also rarely cause human disease. The pathogen infects cucumber and causes cucumber target spot, which has given rise to great yield loss of cucumber in China recently. Genome sequence and spore germination associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola .Results Firstly, we reported the draft genome sequences of a cucumber-sampled C. cassiicola isolate HGCC with high virulence. Although being conspecific, HGCC had distinct difference with a rubber-sampled isolate (CCP) and a human-sampled isolate (UM591) in genome sequences. The proportion of secreted proteins was 7.4% in HGCC. 28.6% of HGCC predicted genes were highly homologous to experimentally proven virulence-associated genes, which was close to that in CCP, UM591 and some plant fungal pathogens, but far more than 21.9% in Phaeosphaeria nodorum and 19.6% in Botrytis cinerea . Thousands of putative virulence-associated genes in various pathways or families were identified in HGCC. Secondly, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-seq). A total of 3,288 differentially expressed genes (DEGs) were identified. The majority of KEGG annotated DEGs were involved in metabolism, genetic information processing, cellular processes, organismal system, human diseases and environmental information processing.Conclusions These results not only facilitated the exploration of the molecular pathogenic mechanism of C. cassiicola to cucumber and the understanding of molecular and cellular processes during spore germination, but also laid the foundation for the disease control.