New Fusarium Strain Decimated Farmed Prawns in South China, Genome Reveals

A newly isolated fungus that swept through farmed Pacific whiteleg shrimp (Penaeus vannamei) in South China, leaving black plaques across the bodies of infected animals and causing heavy economic losses, has now had its entire genome sequenced and dissected. The strain, designated 1-Jan and described in Current Genetics, was recovered from diseased prawns weighing roughly 50 grams, and laboratory infection experiments confirmed that it reproduces the fatal disease seen on farms.

The researchers began by isolating the fungus from lesions on diseased prawns, which showed black spots on the gills and dark brown ulcerative lesions on the carapace and appendages. Microscopic examination of affected tissue revealed fungal hyphae and crescent-shaped spores, and cultures grown on potato dextrose agar produced colonies composed of hyphae and spores whose three-septate spore morphology is characteristic of Fusarium.

Over an eight-day observation period, the infected animals developed black gill disease mirroring the symptoms of naturally diseased individuals. Microscopy of gill filaments from infected shrimp showed abundant fungal hyphae, whereas no abnormalities appeared in controls, and infection significantly reduced shrimp survival. Critically, the fungus re-isolated from experimentally infected shrimp was genetically identical to the original challenge strain, satisfying the criteria for identifying 1-Jan as the causative agent of the disease.

The final assembly spans 51.8 megabases across 54 scaffolds with an N50 length of 1,974 kilobases and a GC content of 51.73 percent, achieved at roughly 62-fold read coverage from 873,391 subreads totaling more than 9.8 billion base pairs. Gene prediction with AUGUSTUS identified 9,769 putative genes averaging 1,282 base pairs in length and occupying 24.17 percent of the genome.

Functional annotation painted a picture of a metabolically versatile fungus. Ninety-four percent of predicted proteins received annotations in the comprehensive NR database, 58.8 percent acquired Gene Ontology terms dominated by catalytic activity, binding, and metabolic process, and 43.9 percent mapped to KEGG pathways, with transport and catabolism, signal transduction, translation, and amino acid and carbohydrate metabolism among the most prominent categories. Twenty-two percent of proteins aligned to KOG orthologous clusters, and 32.9 percent mapped to Swiss-Prot. Repeat analysis uncovered 699 LINEs, 14 SINEs, 1,503 long terminal repeats, 1,570 DNA transposons, and 5,199 tandem repeats, while non-coding RNA prediction identified 306 transfer RNAs and numerous ribosomal RNA genes.

The core of the study lies in its search for pathogenicity factors. Annotation against the PHI database of experimentally verified pathogen-host interaction genes yielded 1,101 hits, including genes in the lethal, increased virulence, and enhanced antagonism categories, with the GFA1 gene, originally characterized in the human pathogen Aspergillus fumigatus, producing the most significant alignment. The fungal cytochrome P450 database contributed 126 annotations, the fungal virulence factor database DFVF added 479, and the carbohydrate-active enzyme database CAZy contributed 497 annotations, including 225 glycoside hydrolases. The authors note that these database hits identify candidate genes whose actual roles in shrimp infection remain to be tested experimentally.

Comparative genomics placed 1-Jan in its evolutionary context. A phylogenetic tree built from an SNP matrix against eight reference genomes, including F. solani JS-169, F. solani IMV00293, Nectria haematococca, F. virguliforme, F. graminearum, F. verticillioides, F. oxysporum, and F. proliferatum, placed 1-Jan on the same branch as F. solani JS-169, N. haematococca, and F. virguliforme. Genome-wide collinearity analysis independently confirmed that 1-Jan shows the highest similarity to N. haematococca, with F. solani JS-169 second. Orthologous clustering across the nine genomes generated 12,699 gene families, of which 3,052 were single-copy families shared across all genomes, indicating that despite being a newly recognized shrimp pathogen, 1-Jan shares a common ancestry with known F. solani complex strains.

By intersecting these comparative data with the pathogenicity annotations, the team narrowed the candidate list. Within the 1-Jan genome, 737 genes carried SNP mutation sites, 241 of which are potential pathogenicity factors, and of the 4,255 single-copy genes in the core gene clusters, 859 were classified as potentially pathogenic. Indel analysis against the three closest reference genomes flagged additional candidates, including 736 pathogenicity-factor genes with indel sites in F. solani JS-169.

That chitin connection may explain the disease itself. Because 1-Jan was isolated from dead shrimp while its three closest sequenced relatives are known plant pathogens, the authors suggest that the capacity to degrade chitin is likely essential to this strain’s metabolism of its crustacean host and a plausible driver of its pathogenicity, though they emphasize that the exact roles of GFA1 and the other predicted pathogenicity genes require further investigation.

The study also catalogued secondary metabolite gene clusters, finding that the type I polyketide synthase cluster for Fusarubin is shared among the four compared strains while Gibepyrone A is absent from 1-Jan but present in the other three. For aquaculture, the practical significance is twofold: whole-genome sequencing overcomes the unreliability of morphology-based Fusarium identification, since spore and colony traits are prone to mutation, and the genome sequence plus the catalogued candidate pathogenicity genes provide a molecular foundation for understanding Fusarium-induced disease in prawns. The authors frame these resources as steps toward better management of fungal infections in shrimp farming, where high stocking density, injuries, and poor water quality all raise infection risk, though translating genomic candidates into validated drug or breeding targets will require the functional experiments this descriptive genome study deliberately leaves to future work.

Subject of Research: Whole-genome sequencing and comparative analysis of a novel Fusarium solani strain pathogenic to Pacific whiteleg shrimp

Article Title: Genomic characterization and analysis of Fusarium Solani isolate 1-Jan, a novel pathogenic strain infecting Penaeus vannamei

Article References: Ge, H., Wu, Q., Ning, Y., Wu, L., Li, H., Wen, P., Guo, X., Wang, W., Wang, X., Li, M., Dai, Y., Lin, X., & Lin, Q. (2025). Genomic characterization and analysis of Fusarium Solani isolate 1-Jan, a novel pathogenic strain infecting Penaeus vannamei. Current Genetics, 71(1), Article 24. https://doi.org/10.1007/s00294-025-01323-y

Image Credits: AI Generated

DOI: 10.1007/s00294-025-01323-y

Keywords: Fusarium solani, Penaeus vannamei, whole-genome sequencing, comparative genomics, pathogenicity genes, chitinase, aquaculture, shrimp disease, PacBio sequencing, PHI database, black gill disease, South China