van Westerhoven Anouk C, Fokkens Like, Wissink Kyran, Kema Gert H J, Rep Martijn, Seidl Michael F
Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3583CH, Utrecht, the Netherlands.
Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands.
NAR Genom Bioinform. 2025 Apr 2;7(2):lqaf034. doi: 10.1093/nargab/lqaf034. eCollection 2025 Jun.
Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for 73 diverse genomes, a major fungal plant pathogen with a compartmentalized genome that includes conserved core as well as variable accessory chromosomes. To obtain insights into accessory chromosome dynamics, we first constructed a chromosome similarity network using all-vs-all similarity mapping. We identified eleven core chromosomes conserved across all strains and a substantial number of highly variable accessory chromosomes. Some of these accessory chromosomes are host-specific and likely play a role in determining host range. Using a k-mer based approach, we further identified the presence of these accessory chromosomes in all available (581) assemblies and corroborated the occurrence of host-specific accessory chromosomes. To further analyze the evolution of chromosomes in , we constructed a pangenome variation graph per group of homologous chromosomes. This reveals that accessory chromosomes are composed of different stretches of accessory regions, and possibly rearrangements between accessory regions gave rise to these mosaic accessory chromosomes. Furthermore, we show that accessory chromosomes are likely horizontally transferred in natural populations. Our findings demonstrate that a pangenome variation graph is a powerful approach to elucidate the evolutionary dynamics of accessory chromosomes in , which is not only a useful resource for but also provides a framework for similar analyses in other species containing accessory chromosomes.
在一个物种的部分而非所有个体中发现的额外染色体，在真菌植物病原体的致病性和宿主特异性方面发挥着重要作用。然而，它们的变异性使基于参考基因组的分析变得复杂，尤其是当这些染色体在参考基因组中缺失时。泛基因组变异图为研究这些染色体提供了一种无需参考基因组的替代方法。在这里，我们为73个不同的基因组构建了一个泛基因组变异图，这是一种具有分隔基因组的主要真菌植物病原体，其基因组包括保守的核心染色体以及可变的额外染色体。为了深入了解额外染色体的动态变化，我们首先使用全对全相似性映射构建了一个染色体相似性网络。我们鉴定出了在所有菌株中都保守的11条核心染色体以及大量高度可变的额外染色体。其中一些额外染色体具有宿主特异性，可能在决定宿主范围方面发挥作用。使用基于k-mer的方法，我们进一步在所有可用的（581个）组装体中鉴定出了这些额外染色体的存在，并证实了宿主特异性额外染色体的出现。为了进一步分析某物种中染色体的进化，我们为每组同源染色体构建了一个泛基因组变异图。这表明额外染色体由不同的额外区域片段组成，并且额外区域之间的重排可能产生了这些镶嵌的额外染色体。此外，我们表明额外染色体可能在自然种群中水平转移。我们的研究结果表明，泛基因组变异图是阐明某物种中额外染色体进化动态的有力方法，这不仅是某物种的有用资源，也为其他含有额外染色体的物种的类似分析提供了框架。
