Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus

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.

Detection and Quantification of Stagonosporopsis cucurbitacearum in Seeds of Cucurbita maxima Using Droplet Digital Polymerase Chain Reaction

“…Healthy seeds are the start of healthy plants, and this is an essential requirement to safeguard the productivity of crops. GSB is a widespread disease and leads to significant losses in yield and quality for cucurbit crops worldwide ( Keinath, 2011 ; Li et al, 2015 ; Yao et al, 2016 ; Zhao et al, 2020 ). In addition, the use of grafted cucurbits further increases the risk of GSB development from seedborne inoculum.…”

“…In the Mediterranean areas as well in Asia, S. cucurbitacearum was described as the main pathogenic fungus of Cucurbita maxima seedling related to GSB, able to reduce both squash yield and quality ( Moumni et al, 2019 , 2020 ; Zhao et al, 2020 ). In warm and humid environments, infections of these fungi can result 15 to 50% in reduction of yields and rapid death of the cucurbit plants ( Keinath et al, 1995 ; Boughalleb et al, 2007 ; Keinath, 2011 ; Li et al, 2015 ; Yao et al, 2016 ; Moumni et al, 2019 ; Zitter and Kyle, 1992 ).…”

“…For these reasons, the production and the movement of seeds represent a particularly efficient vehicle to disperse such seedborne pathogens ( Zhang et al, 2018 ; Moumni et al, 2020 ; Zhao et al, 2020 ). Also, as global trade has increased, so has the movement of seeds and other plant materials between countries, thus increasing the risk of the transport and transfer of plant pathogens ( Epanchin-Niell and Hastings, 2010 ; Mancini and Romanazzi, 2014 ; Mancini et al, 2016 ).…”

Evaluation of Seven Essential Oils as Seed Treatments against Seedborne Fungal Pathogens of Cucurbita maxima

“…This association between seeds and pathogens is an important means for the pathogens to spread on a large scale and a way to guarantee their survival in nature [ 7 , 8 , 9 ]. Seedborne pathogens can limit the production of many crops and can result in severe economic losses to growers [ 10 , 11 , 12 , 13 ].…”

“…are devastating fungal pathogens of cucurbits and can lead to severe yield losses. These pathogens are major seedborne fungi of pumpkin and the dominant fungal cause of pumpkin seedling gummy stem blight [ 11 , 30 ]. No commercial cultivars with resistance to gummy stem blight are available, and so this disease has been frequently managed by fungicides application.…”