Data_Sheet_6_Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece.XLSX

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，作为一种导致开心果Septoria叶斑病的病原菌，在全球范围内对开心果种植造成了巨大的经济损失。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——共计27个分离株，其中每个地区单元（皮里亚、拉里萨和法提奥蒂达）各有9个分离株。参考分离株（SPF8）组装成的基因组总大小为43.1兆碱基对，其中38.6%位于富含AT碱基对的区域，约37.5%的G:C比。这27个分离株的基因组平均含有42%的编码基因和20%的重复区域。基于单核苷酸多态性（SNP）衍生出的树状图显示，来自法提奥蒂达南部地区的分离株彼此之间似乎比其他地区的分离株更具有差异性，并且也包含了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之间差异较小，且区分度较低。无性繁殖似乎是典型特征，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，其具有半寄生和腐生适应性，与其长期的潜伏期相一致。基因预测和直系同源聚类生成了一个包含21,174个位点位的全基因组基因集合。共预测了59个直系同源群可能含有候选效应蛋白，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性，要么可以从保守结构域的匹配中分配预测功能。总的来说，效应蛋白的预测表明，S. pistaciarum采用了一种防御性效应蛋白与抑制宿主防御作用相结合的策略，以及具有多种细胞毒活性的进攻性效应蛋白。一些类似效应蛋白的直系同源群呈现出同一蛋白的变异版本，这表明可能发生了地区特异性适应性。这些发现为揭示S. pistaciarum的致病机制和种群动态提供了见解，并为有效管理开心果的Septoria叶斑病提供了未来的研究方向。