Data_Sheet_7_Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece.FASTA

Septoria pistaciarum, a causal agent of Septoria leaf spot disease of pistachio, is a fungal pathogen that causes substantial losses in the cultivation, worldwide. This study describes the first pan-genome-based survey of this phytopathogen—comprising a total of 27 isolates, with 9 isolates each from 3 regional units of Greece (Pieria, Larissa and Fthiotida). The reference isolate (SPF8) assembled into a total of 43.1 Mb, with 38.6% contained within AT-rich regions of approximately 37.5% G:C. The genomes of the 27 isolates exhibited on average 42% gene-coding and 20% repetitive regions. The genomes of isolates from the southern Fthiotida region appeared to more diverged from each other than the other regions based on SNP-derived trees, and also contained isolates similar to both the Pieria and Larissa regions. In contrast, isolates of the Pieria and Larissa were less diverse and distinct from one another. Asexual reproduction appeared to be typical, with no MAT1-2 locus detected in any isolate. Genome-based prediction of infection mode indicated hemibiotrophic and saprotrophic adaptations, consistent with its long latent phase. Gene prediction and orthology clustering generated a pan-genome-wide gene set of 21,174 loci. A total of 59 ortholog groups were predicted to contain candidate effector proteins, with 36 (61%) of these either having homologs to known effectors from other species or could be assigned predicted functions from matches to conserved domains. Overall, effector prediction suggests that S. pistaciarum employs a combination of defensive effectors with roles in suppression of host defenses, and offensive effectors with a range of cytotoxic activities. Some effector-like ortholog groups presented as divergent versions of the same protein, suggesting region-specific adaptations may have occurred. These findings provide insights and future research directions in uncovering the pathogenesis and population dynamics of S. pistaciarum toward the efficient management of Septoria leaf spot of pistachio.

Septoria pistaciarum，即榛树叶斑病的病原菌，是一种导致全球榛树栽培遭受重大损失的真菌病原体。本研究首次对这一植物病原菌进行了基于全基因组范围的调查，共包括27个分离株，其中每个区域单位（皮里亚、拉里萨和弗西奥蒂达）各有9个分离株。参考分离株（SPF8）组装成的总大小为43.1兆碱基对，其中38.6%位于富含AT区域的约37.5%的G:C含量。27个分离株的基因组平均含有42%的基因编码区和20%的重复区域。基于单核苷酸多态性（SNP）衍生的系统发育树显示，来自南方弗西奥蒂达地区的分离株之间的差异似乎比其他地区更大，并且还包含与皮里亚和拉里萨地区相似的分离株。相比之下，皮里亚和拉里萨地区的分离株在多样性和差异性方面较小。无性繁殖似乎是典型的繁殖方式，因为在任何分离株中均未检测到MAT1-2位点。基于基因组的感染模式预测表明，存在半寄生和腐生适应性，这与其长期潜伏期相一致。基因预测和同源聚类生成了一个包含21,174个位点的全基因组基因集合。共预测了59个直系同源群可能包含候选效应蛋白，其中36个（61%）要么与来自其他物种的已知效应蛋白具有同源关系，要么可以通过与保守结构域的匹配预测到预测功能。总体而言，效应蛋白的预测表明，S. pistaciarum利用具有抑制宿主防御功能的防御性效应蛋白和具有多种细胞毒性活性的攻击性效应蛋白的组合。一些类似效应蛋白的直系同源群呈现为同一蛋白质的变异版本，这表明可能发生了特定地区的适应性进化。这些发现为揭示S. pistaciarum的致病性和种群动态提供了见解，并为高效管理榛树叶斑病提供了未来的研究方向。