Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen.
Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen.
复制标题
不同的基因组背景预测真菌植物病原体不同致病型中基因存在与缺失的变异。
DOI：
10.1101/2023.02.17.529015
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Krasileva,KseniaV
中科院分区：
文献类型：
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作者：
Joubert,PierreM;Krasileva,KseniaV
背景真菌利用其泛基因组的附属片段来适应环境。虽然基因存在-不存在变异（PAV）有助于形成这些辅助基因库，但这些事件是否发生在特定的基因组背景下仍不清楚。此外，由于泛基因组研究通常将同一物种的所有成员分组在一起，因此不确定塑造泛基因组进化的基因组或表观基因组特征是否在同一物种内的种群之间一致。真菌植物病原体是回答这些问题的有用模型，因为同一物种的成员经常感染不同的宿主，并且它们经常依赖基因PAV来适应这些宿主。结果通过对稻瘟病菌PAV基因的分析，发现PAV的致病效应基因、抗生素产生基因和非自我识别基因可能驱动稻瘟病菌对环境的适应。然后，我们分析了基因组和表观基因组特征以及来自可用数据集的数据，以寻找可能有助于解释这些PAV事件的模式。我们观察到，接近转座因子（TE），基因GC含量，基因长度，在宿主中的表达水平，和组蛋白H3 K27 me 3标记之间的PAV基因和保守基因，在其他功能不同。我们利用这些特征构建了一个随机森林分类器，该分类器能够以高精度（86.06%）和召回率（92.88%）预测一个基因是否可能在水稻感染M中经历PAV。米。最后，我们发现PAV在小麦和水稻的致病型M。它们的数量和基因组背景不同。结论PAV基因的基因组和表观基因组特征可用于更好地理解和预测真菌泛基因组进化。我们还表明，大量的物种内的变化可以存在于这些功能。
Background Fungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts. Results We analyzed gene PAV in the rice and wheat blast fungus, Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infecting M. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes of M. oryzae differed in their number and their genomic context. Conclusions Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.