Whole-Genome Sequencing and Comparative Genome Analysis of Fusarium solani-melongenae Causing Fusarium Root and Stem Rot in Sweetpotatoes

Abstract

ABSTRACT Sweetpotato (Ipomoea batatas) is the eighth most important crop globally. However, the production and quality of sweetpotatoes are threatened by Fusarium diseases that are prevalent around the world. In this study, a Fusarium species that causes root and stem rot in sweetpotatoes was studied. The pathogenic fungus CRI 24-3 was isolated and sequenced using third- and next-generation sequencing techniques and a 49.6 Mb chromosome-level draft genome containing 15,374 putative coding genes were obtained. Molecular phylogenetic analysis showed that CRI 24-3 was an F. solani-melongenae strain within clade 3 of the F. solani species complex (FSSC). CRI 24-3 showed a relatively high number of virulence factors, such as carbohydrate-active enzymes (CAZymes), pathogen-host interaction (PHI) proteins, and terpene synthases (TSs), compared with the number of those identified in other sequenced FSSC members. Comparative genome analysis revealed considerable conservation and unique characteristics between CRI 24-3 and other FSSC species. In conclusion, the findings in the current study provide important genetic information about F. solani-melongenae and should be useful in the exploration of pathogenicity mechanisms and the development of Fusarium disease management strategies. IMPORTANCE Fusarium root and stem rot in sweetpotato are prevalent in the main sweetpotato-growing areas in China, and fungal isolation, morphological characteristics, and molecular phylogenetic analysis of the disease causal agent (F. solani-melongenae isolate CRI 24-3) were systematically studied. The genome sequence of F. solani-melongenae isolates CRI 24-3 was first reported, which should provide a basis for genome assembly of other closely related Fusarium species. Carbohydrate-active enzymes predicted in CRI 24-3 may be important to convert the substantial polysaccharides to sustainable and renewable energy. Moreover, other virulence factors facilitating Fusarium diseases, including effectors and toxic secondary metabolites, are ideal objects for pathogenicity mechanism research and molecular targets for fungicide development. The findings of comparative genome analysis of CRI 24-3 and 15 sequenced members of the F. solani species complex help promote an integral understanding of genomic features and evolutionary relationships in Fusarium.

Keywords

• Fusarium solani-melongenae
• Fusarium solani species complex
• genome sequencing
• comparative genome analysis
• Fusarium root and stem rot
• sweetpotato