Whole-genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Neoscytalidium dimidiatum on pitaya

Neoscytalidium dimidiatum (class Dothideomycetes) is a fungus responsible for canker disease in pitaya stems and fruits, leading to significant economic losses. However, little is known about the pathogenesis, family evolution, and genetic variants of this species. In this study, we report a high-quality genome sequence of N. dimidiatum based on the Nanopore sequencing technology platform for sequencing and Hi-C assembly technology for genome assembly. The genome contains 12 chromosomes (2n = 2x = 12; diploid), with a sequencing depth of 186.1x, encoding 12,349 proteins. Molecular phylogenetic analysis showed that N. dimidiatum is evolutionarily close to Botryosphaeria dothidea. Compared to other fungi, the N. dimidiatum genome contains many carbohydrate-active enzymes and secondary metabolites. Additionally, we predict that N. dimidiatum contains 121 candidate effectors that may play important roles in infection and colonization, promoting pathogenicity in pitaya. Nine of these effectors were confirmed to contain signal peptides and inhibit BAX/INF1-induced necrosis in Nicotiana benthamiana, demonstrating their importance during infection. Finally, we also confirm that N. dimidiatum does not form an appressorium or infection thread but instead infects pitaya via open stomata. In conclusion, the results provide a foundation for future research on N. dimidiatum and the control of pitaya canker.

Automated summary

This study reports a high-quality genome sequence of Neoscytalidium dimidiatum and reveals its evolutionary relationship, genomic features, and candidate effectors. It also confirms that N. dimidiatum infects pitaya through open stomata.