Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans , an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum

is a mycoparasite of the notorious plant pathogen . To further understand the parasitism of , we assembled and analysed its genome and performed transcriptome analyses. The genome of strain ZS-1 was assembled into 350 scaffolds and had a size of 39.8 Mb. A total of 11 437 predicted genes and proteins were annotated, and 30.8 % of the blast hits matched proteins encoded by another member of the Pleosporales, , a worldwide soilborne fungus with biocontrol ability. The transcriptome of strain ZS-1 during the early interaction with at 0, 4 and 12 h was analysed. The detected expressed genes were involved in responses to host defenses, including cell-wall-degrading enzymes, transporters, secretory proteins and secondary metabolite productions. Seventeen differentially expressed genes (DEGs) of fungal cell-wall-degrading enzymes (FCWDs) were up-regulated during parasitism, with only one down-regulated. Most of the monocarboxylate transporter genes of the major facilitator superfamily and all the detected ABC transporters, especially the heavy metal transporters, were significantly up-regulated. Approximately 8 % of the 11 437 proteins in were predicted to be secretory proteins with catalytic activity. In the molecular function category, hydrolase activity, peptidase activity and serine hydrolase activity were enriched. Most genes involved in serine hydrolase activity were significantly up-regulated. This genomic analysis and genome-wide expression study demonstrates that the mycoparasitism process of is complex and a broad range of proteins are deployed by to successfully invade its host. Our study provides insights into the mechanisms of the mycoparasitism between and and identifies potential secondary metabolites from for application as a biocontrol agent.