Transcriptome analysis reveals the mechanism by which the biocontrol fungus Chaetomium globosum CEF-082 controls Verticillium wilt in cotton

Abstract Background: Verticillium wilt of cotton is a serious soil-borne disease that causes a substantial reduction in cotton yield. A previous study showed that the endophytic fungus Chaetomium globosum CEF-082 could control Verticillium wilt of cotton, but the molecular mechanism by which CEF-082 controls Verticillium wilt is still unknown. Results: To study the mechanism by which CEF-082 controls Verticillium wilt, the transcriptome of cotton seedlings pretreated with CEF-082 was sequenced. The results revealed 5638 DEGs 24 h post-inoculation with CEF-082, and 2921 and 2153 DEGs 12 and 48 h post-inoculation with Verticillium dahliae , respectively. At twenty-four hours post-inoculation with CEF-082, KEGG enrichment analysis indicated that the DEGs were mainly enriched in plant-pathogen interaction, MAPK signalling pathway-plant, flavonoid biosynthesis, and phenylpropanoid biosynthesis. There were 1209 DEGs specifically induced after inoculation with CEF-082 and V. dahliae . GO enrichment indicated that these DEGs were mainly enriched in the terms reactive oxygen species metabolic process, hydrogen peroxide metabolic process, defence response, superoxide dismutase activity, and antioxidant activity. Here, many genes, such as ERF, CNGC, FLS2, MYB, GST and CML, were identified that regulate crucial points in defence-related pathways and that may contribute to V. dahliae resistance in cotton. These results provide a basis for the understanding of the molecular mechanism by which biocontrol fungi control Verticillium wilt. Conclusions: In this study, we found that CEF-082 could regulate multiple metabolic pathways in cotton. After treatment with Verticillium dahliae , the defence response of cotton plants pre-inoculated with CEF-082 was strengthened.