The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.

Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

与其他多年生木本植物一样，葡萄树（ Vitis vinifera L.）的永久器官被各种不相关的致病性子囊菌定植，这些真菌分泌细胞壁降解酶和植物毒性次生代谢物，导致宿主受损和疾病症状。躯干病原体在引起的症状以及损害的程度和速度方面有所不同。即使在同一葡萄园内，同一物种的分离株通常表现出广泛的毒力范围。本研究重点关注Eutypa lata、Neofusicocum parvum和Phaeoacremium mini，它们分别是Eutypa 顶枯病、Botryosphaeria 顶枯病和Esca 的致病因子。我们对来自全球葡萄栽培区的 50 个分离株进行了测序，并为每个物种构建了核苷酸水平、无参考的泛基因组。通过检查基因组多样性和全基因组结构，我们分析了假定毒力因子的种内保守性和变异性，重点关注正选择下的功能以及最近基因家族收缩和扩张的动态。我们的研究结果揭示了每个全基因组的核心基因组、可有可无的基因组和私有基因组中假定的毒力因子的对比分布。例如，碳水化合物活性酶（CAZymes）普遍存在于每个全基因组的核心基因组中，而生物合成基因簇普遍存在于E. lata和P. minimary的可有可无的基因组中。在正选择下，可有可无的级分也富集了吉普赛转座元件和毒力因子（E. lata和P. minimum中的聚酮合酶基因，N. parvum中的糖基转移酶）。我们的研究结果强调了每个物种基因组结构的复杂性，并提供了对其适应性策略的见解，增强了我们对潜在毒力机制的理解。

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