Nuclei define eukaryotes, enabling macromolecular compartmentalization and cellular regulation. Each nucleus is believed to contain one or more haploid sets of chromosomes (1N). However, we discovered that haploid cells of the pathogenic fungi Sclerotinia sclerotiorum and Botrytis cinerea distribute their chromosomes such that each of their nuclei contains only a subset of the haploid chromosomes (≤½N). The unusual chromosomal distribution was confirmed by cellular and molecular methods including chromosome counting, fluorescence in situ hybridization, flow cytometry–based DNA measurements, and single-nucleus polymerase chain reaction experiments. This phenomenon challenges fundamental assumptions about nuclear organization and opens fresh avenues in chromosome biology.

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations in SsATG1, SsATG2, SsATG4, SsATG5, SsATG9, and SsATG26. Functional validation through gene knockouts revealed that each ATG is essential for sclerotia formation, although the morphology of appressoria was not significantly altered in the mutants. Different levels of virulence attenuation were observed among these mutants. Autophagy, monitored using GFP-ATG8, showed dynamic activities during sclerotia development. These findings suggest that macroautophagy and pexophagy contribute to sclerotia maturation and virulence processes. Future work will reveal how autophagy controls target organelle or protein turnover to regulate these processes.

Sclerotinia sclerotiorum is a devastating soilborne fungal pathogen that causes Sclerotinia stem rot in many economically important crops. It forms sclerotia, resilient dormant structures that can persist in soil for years. Understanding the molecular mechanism of sclerotia formation is crucial for developing effective control strategies, but only a limited number of signaling components have been uncovered in this process. Through independent forward genetic screens, we identified SsLae1 and SsVel1, two core components of the conserved fungal velvet complex, as essential regulators of sclerotia formation and virulence in S. sclerotiorum. Disruption of either gene abolished sclerotia formation, impaired compound appressorium development, and significantly reduced virulence. Further RNA-seq analysis using the Ssvel1 mutant revealed widespread downregulation of known developmental and virulence regulators. Collectively, these findings establish the velvet complex as a master regulator for both sclerotia development and virulence in S. sclerotiorum.

The nucleus is a defining feature of eukaryotic cells, compartmentalizing the genome to enable precise regulation of diverse cellular processes. The long-standing paradigm in textbooks states that each nucleus carries at least a complete haploid genome —the “one nucleus, one whole genome” rule. A striking exception was recently uncovered: in two sclerotia-forming plant pathogenic fungi in the Sclerotiniaceae family, Sclerotinia sclerotiorum and Botrytis cinerea , haploid chromosomes are irregularly distributed across multiple nuclei. However, whether such phenomenon occurs in other eukaryotes, particularly in non-pathogenic fungi, is unclear. Through a literature survey, we identified many fungi that can potentially also separate their haploid chromosomes across different nuclei. Interestingly, Neurospora crassa , a foundational fungal genetics model, came out as a candidate. Its conidia, typically containing two or three nuclei, were believed to harbor a complete haploid genome within each nucleus. However, using approaches including chromosome counting, flow cytometry, and fluorescence in situ hybridization, we found that haploid chromosomes in N. crassa can be unevenly distributed among multiple nuclei. These findings challenge longstanding assumptions in fungal genetics and provide new directions for investigating genome organization. Our results indicate that the organisms violating the “one nucleus, one whole genome” rule are beyond sclerotia-forming pathogenic fungi. Since over 90% of fungi have not even been described, we propose that many more of them may likewise partition their genomes non-uniformly across nuclei, a process that could facilitate their adaptation and evolution.