Breaking the ''one nucleus, one whole genome'' rule: Neurospora crassa separates its haploid chromosomes into different nuclei

Abstract

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.