In the ever-evolving world of fungal genetics, a fascinating mechanism has captured the attention of researchers worldwide: the horizontal transfer of accessory chromosomes. Unlike the traditional vertical passage of genetic material from parent to offspring, this process involves the movement of entire chromosomes between distinct fungal genomes, challenging previous understandings of genetic exchange. Recent investigations into accessory chromosomes—genomic elements distinct from the essential core chromosomes—have unveiled how these modular genetic units might transverse species boundaries, potentially reshaping fungal diversity and adaptation.
Accessory chromosomes are unique. Found alongside the stable core genomes across numerous fungal species, these chromosomes often harbor genes linked to pathogenicity, environmental adaptability, and other specialized functions. Despite being dispensable under certain conditions, accessory chromosomes wield significant influence over fungal biology and evolution. Yet, the nuances underlying their transmission remain enigmatic. Horizontal chromosome transfer (HCT), wherein these accessory chromosomes leap between genomes, offers a tantalizing glimpse into how fungi can rapidly acquire new traits and respond to environmental pressures.
Although accessory chromosomes have been documented in over 25 fungal species, direct evidence of such horizontal transfers has previously been confined to just five species. This disparity raises a critical question: could accessory chromosomes in other fungi have undergone horizontal transfers that elude current detection methods? To address this, scientists have turned to molecular signatures embedded within the chromosomes themselves—specifically, variations in codon usage bias, a subtle but telling hallmark of genomic origin and evolutionary history.
Codon usage bias reflects the preference for certain synonymous codons over others during protein synthesis. Introduced by Sharp and Li in 1986, the relative synonymous codon usage (RSCU) index has since become an indispensable metric to probe genetic and evolutionary dynamics. Codon preferences can be shaped by myriad forces, ranging from mutational biases such as nucleotide composition and sequence context, to selective pressures optimizing translational accuracy and efficiency. Indeed, in fungi, processes like Repeat-Induced Point (RIP) mutations modulate codon compositions uniquely for accessory chromosomes, potentially serving as fingerprint-like indicators of their evolutionary journey.
The intriguing hypothesis posits that if an accessory chromosome originates from one fungal species and subsequently integrates into another genome through HCT, its codon usage bias might starkly contrast with that of the recipient’s core chromosomes. Essentially, the passenger chromosome carries the mutational and selective imprints of its species of origin, creating a detectable mismatch. This differential bias thereby serves as a genomic clue, hinting at past horizontal transfers.
Empirical evidence supports this notion. Several fungal species with documented HCT events—including strains of Fusarium oxysporum, Fusarium vanettenii MPVI, Alternaria arborescens, Colletotrichum graminicola, and Metarhizium robertsii—exhibit marked differences between core and accessory chromosomes in terms of codon usage bias. Such findings underscore the potential universality of these patterns, making RSCU comparisons a promising tool for mapping horizontal transfers beyond the currently known cases.
However, the narrative is complex. Differences in codon bias are not exclusively signatures of horizontal transfer. Mutational landscapes can vary independently between core and accessory chromosomes within the same genome, influenced by factors like chromatin modifications. For example, distinct histone modifications observed on accessory chromosomes might drive higher mutation rates, altering codon usage independently of chromosome transfer events. Furthermore, in sexual species, the smaller effective population size of accessory chromosomes can reduce selection efficiency, subtly reshaping their codon compositions.
Moreover, codon usage bias is not always sensitive at the single-gene level for detecting past horizontal events. Single genes may not retain discernible signals due to homogenization or similar selective pressures in donor and recipient species. Yet, the horizontal transfer of chromosomes involves a substantial array of genes and noncoding elements simultaneously, providing a larger genomic canvas where codon usage differences may be amplified and more readily observed. This scale allows researchers to statistically compare entire core and accessory chromosome gene sets, enhancing detection power.
It is also crucial to emphasize that the absence of significant codon usage differences does not necessarily preclude previous HCT. Transfers between closely related species, sharing similar mutational and selective landscapes, might leave little discernible imprint on codon bias. Hence, researchers caution against relying solely on these molecular signatures. Instead, codon usage comparisons should be integrated with phylogenetic, experimental, and functional analyses to build a comprehensive picture.
Building on this, a recent study undertook a broad comparative analysis of codon usage bias across core and accessory chromosomes in numerous fungal species. This analysis incorporated fungi with previously verified HCT events and extended to those with less characterized accessory chromosome dynamics. Employing robust statistical frameworks and gene annotation methodologies, the study aimed to assess how widespread signals indicative of horizontal transfer are among fungal accessory chromosomes.
Their results present a compelling landscape: fungal strains with experimentally confirmed HCT displayed pronounced codon usage differences between core and accessory chromosomes, while several other species showed subtler yet statistically significant discrepancies. By transforming raw RSCU data for enhanced comparability and deploying rigorous correction for multiple testing, the research delineated a spectrum of potential horizontal transfer candidates, expanding the horizon for recognizing genomic exchange in fungi.
Further implications of these findings lie in understanding the evolutionary and ecological ramifications of horizontal chromosome transfer. The modular nature of accessory chromosomes allows fungi to acquire and disseminate traits rapidly, including virulence factors, antibiotic resistance, and metabolic capabilities. This dynamic reshuffling can fuel adaptive radiations and impact pathogenicity, agriculture, and ecosystem functioning significantly.
Delving deeper, the study acknowledges that accessory chromosome biology is entwined with chromatin architecture and epigenetic landscapes. Histone modifications, for example, not only influence mutation rates but may regulate the transfer competence themselves. This intertwining of genomic structure and transfer process hints at regulatory mechanisms controlling HCT, moving beyond random events to possibly orchestrated genetic exchanges.
The study’s integrative approach, combining codon bias analysis with comparative genomics and functional annotations, sets a precedent for fungal genetics research. It calls for expanded sequencing efforts distinguishing core and accessory chromosomes across diverse fungal taxa, enabling finer resolution of HCT patterns and their biological outcomes.
In conclusion, horizontal chromosome transfer represents a paradigm-shifting mechanism in fungal evolution, leveraging accessory chromosomes as vehicles of rapid genetic innovation. While codon usage bias serves as a powerful lens to detect these transfers, its interpretation requires nuance and corroboration from complementary evidence. As genomic technologies advance, unearthing the complexities of accessory chromosome dynamics will illuminate fundamental processes shaping fungal biodiversity, with far-reaching implications in biology, medicine, and agriculture.
Subject of Research: Horizontal chromosome transfer and codon usage bias in fungal accessory chromosomes
Article Title: Horizontal transfer of accessory chromosomes in fungi – a regulated process for exchange of genetic material?
Article References:
Habig, M., Patneedi, S.K., Stam, R. et al. Horizontal transfer of accessory chromosomes in fungi – a regulated process for exchange of genetic material?. Heredity (2025). https://doi.org/10.1038/s41437-025-00746-0
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41437-025-00746-0
Keywords: Horizontal chromosome transfer, accessory chromosomes, fungi, codon usage bias, relative synonymous codon usage (RSCU), fungal genomics, evolutionary genetics, Repeat-Induced Point mutation, translational selection
