Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean

Abstract

Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C. sojina genome, when compared with other phytopathogenic fungi. Bioinformatics analysis reveals that C. sojina harbours about 752 secreted proteins, and 233 of them are effectors. During early infection, the genes for metabolite biosynthesis and effectors are significantly enriched, suggesting that they may play essential roles in pathogenicity. We further identify 13 effectors that can inhibit BAX-induced cell death. Taken together, our results provide insights into the infection mechanisms of C. sojina on soybean.

Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1 and BdPV1

“…Our investigations revealed that the complete genome sequence size of the B. dothidea LW-Hubei isolate is 46.34 Mb (Table 1). This is larger than the genome sizes of sequenced but not annotated Botryosphaeriaceae taxa B. dothidea and N. parvum isolates with similar genome sizes (42.6 Mb to 45.26 Mb), and low proportions of repeat sequences determined using the NGS method (Bodega and Orlando 2014;van der Nest et al 2014;Liu et al 2016;Luo et al 2018;Yan et al 2018). In particular, the assembled B. dothidea LW-Hubei isolate genome contains 4.31 Mb repetitive sequences, representing a relatively high proportion (9.41%) of the complete genome in Botryosphaeriaceae (Table 2, Fig.…”

“…The repeat sequences were randomly distributed across the full genome of B. dothidea LW-Hubei isolate. It was recently reported that DNA methylation may be involved in host cell processes, such as regulation gene transcription in fungal species (Luo et al 2018;Plissonneau et al 2018;Yan et al 2018). The m6A and m4C in B. dothidea were predicted for the first time using SMRT, which revealed larger numbers of m4C in the genome, occurring at a frequency of 8082/Mb, while m6A was detected at a frequency of 434/Mb.…”

“…It was recently reported that DNA methylation may exist in fungi (Luo et al 2018). In total, 374,995 m4C (4-methyl-cytosine) residues, and 20,121 m6A (6-methyl-adenosine) were identified by SMRT analysis (Fig.…”

“…Despite the importance of B. dothidea, little is known about the genetics and pathogenic mechanism of this pathogen (Wang et al 2018a(Wang et al , 2018b. To date, the main strategy used to reveal the mechanism of phytopathogenic infection has involved sequencing of the complete genome and annotation of gene function in fungal diseases such as rice sheath blight, rice blast, and wheat stripe rust pathogen fungus, Cenococcum geophilum and Cercospora sojina (Dean et al 2005;Zheng et al 2013aZheng et al , 2013bDong et al 2015;Peter et al 2016;Luo et al 2018;Plissonneau et al 2018). Similarly, sequencing of the Ustilago esculenta genome and gene annotation revealed the molecular mechanism of the artificial selection and smut fungi-host interaction involved in RNA-silencing in host defense (Ye et al 2017).…”

Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress

“…However, it is uncertain whether C. sojina secrets cercosporin [10]. One study [11] analyzed the transcriptome of the C. sojina strain Race1 under nitrogen starvation stress. During the early stage of infection, the genes involved in pigment biosynthesis were significantly upregulated, and eight cercosporin biosynthesis genes were screened.…”