Abstract
Outbreaks of gummy stem blight (GSB), an emerging seed pumpkin disease, have increased in number and have become more widespread in recent years. Previously we reported that Stagonosporopsis cucurbitacearum (Sc.) is the dominant fungal cause of pumpkin seedling GSB in Northeast China, where it has greatly reduced crop yields in that region. Here, high-throughput whole-genome sequencing and assembly of the Sc. genome were conducted toward revealing pathogenic molecular regulatory mechanisms involved in fungal growth and development. Zq-1 as representative Sc. strain, DNA of Zq-1was prepared for genomic sequencing, we obtained 5.24 Gb of high-quality genomic sequence data via PacBio RS II sequencing. After sequence data was processed to filter out low quality reads, a hierarchical genome-assembly process was employed that generated a genome sequence of 35.28 Mb in size. A total of 9844 genes were predicted, including 237 non-coding RNAs, 1024 genes encoding proteins with signal peptides, 2066 transmembrane proteins and 756 secretory proteins.Transcriptional identification revealed 54 differentially expressed secretory proteins. Concurrently, 605, 130 and 2869 proteins were matched in the proprietary databases Carbohydrate-Active EnZymes database (CAZyme), Transporter Classification Database (TCDB) and Pathogen–Host Interactions database (PHI), respectively. And 96 and 36 DEGs were identified form PHI database and CAZyme database, respectively. In addition, contig00011.93 was an up-regulated DEG involving ATP-binding cassette metabolism in the procession of infection. In order to test relevance of gene predictions to GSB, DEGs with potential pathogenic relevance were revealed through transcriptome data analysis of Sc. strains pre- and post-infection of pumpkin. Interestingly, Sc. and Leptosphaeria maculans (Lm.) exhibited relatively similar with genome lengths, numbers of protein-coding genes and other characteristics. This work provides a foundation for future exploration of additional Sc. gene functions toward the development of more effective GSB control strategies.
Highlights
Outbreaks of gummy stem blight (GSB), an emerging seed pumpkin disease, have increased in number and have become more widespread in recent years
These studies illustrate the power of whole-genome sequencing and genome-wide analysis to greatly facilitate the discovery of fungal pathogenic molecular regulatory networks and disease-causing genes
High-throughput sequencing technology was used for the first time to sequence the genome of S. cucurbitacearum isolate zq-1, an Sc. isolate obtained from a cold region of China
Summary
Outbreaks of gummy stem blight (GSB), an emerging seed pumpkin disease, have increased in number and have become more widespread in recent years. In 2005, the draft genome sequence of Magnaporthe grisea was annotated and released, revealing a variety of secreted proteins, including new virus-related genes and enzymes involved in secondary metabolism Such information has greatly enhanced our understanding of fungal life processes and our ability to predict fungal pathogenic mechanisms[18]. A high quality whole-genome fine map was obtained after genome assembly with a total size of 35.28 Mb. Based on the complete Sc. genome sequence, differentially expressed Sc. genes at the transcriptional level before and after Sc. infection of pumpkin were analyzed, resulting in identification of genes of numerous secreted proteins, plant cell wall degradation enzymes and secondary metabolic enzymes that may play important roles in GSB pathology. The Sc. genome sequence will likely provide additional insights for development of new strategies to control GSB and other fungal diseases of crops
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