Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200–700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.

中文翻译：

---

群体水平深度测序揭示了小麦病原体小麦发酵斑孢菌克隆和有性繁殖的相互作用


病原体对全球粮食安全造成重大挑战。对于一年生作物，病原体必须在每个生长季节从环境来源重新感染。真菌病原体已经进化出混合繁殖策略，以应对定殖生长植物的独特挑战。然而，病原体多样性在生长季节如何演变仍然很大程度上未知。在这里，我们在受主要真菌病原体小麦发酵壳孢感染的单个实验麦田中进行了深度分层采样。我们分析了从 12 个不同品种收集的 177 个分离株的全基因组序列，这些分离株在生长季节的三个时间点在太空中复制，以最大限度地捕获遗传多样性。现场群体高度多样化，每千碱基有 37 个 SNP，连锁不平衡衰减在 200-700 bp 内，有效群体规模很大。通过实验感染，我们在田间种植的优势品种上测试了收集到的分离株的子集。然而，我们发现从同一品种收集的分离株与从其他品种收集的分离株的毒力没有显着差异。大约 20% 的分离株基因型分为 15 个克隆组。在短距离 (<5 m) 处发现了不成比例的克隆对，这与在同一田地中进行的每代扩散距离的实验估计一致。这证实了生长季节期间叶间传播占主导地位。令人惊讶的是，尽管在生长季节繁殖被认为完全是无性繁殖，但克隆水平并没有随着时间的推移而增加。我们的研究表明，病原体在单一领域建立了巨大且稳定的基因库。 监测作物病原体的短期进化变化将为控制疾病提供更持久的策略。