Abstract Phyllosticta citricarpa is a fungal plant pathogen that causes citrus black spot (CBS). This study is the first to use high throughput sequencing (HTS) to study the genetic diversity within a P. citricarpa population. Seventeen isolates from the United States of America were sequenced and their genomes assembled. A pairwise mapping and variant calling analysis were performed on all isolates, and a low number of inter-isolate variants detected. Furthermore, the HTS data was also used to genotype 4029 SSRs in the isolates, and only 57 polymorphic markers were found. These results confirm the clonality of this P. citricarpa population. However, it is not a totally homogeneous group and it was shown that HTS can detect this fine-scale genetic differentiation. The two different approaches, pairwise mapping and variant calling versus SSR detection and in silico genotyping, yielded similar results, dividing the isolates into the same two groups. The results from this study demonstrate the feasibility of HTS and comparative genome analyses to study the genetic diversity and population structure of this fungus.

中文翻译：

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通过重测序和全基因组分析扩展对美国柑橘叶螨种群结构的了解

摘要 柑桔叶霉是引起柑橘黑斑病（CBS）的真菌植物病原体。本研究首次使用高通量测序 (HTS) 来研究柑橘假单胞菌种群内的遗传多样性。对来自美利坚合众国的 17 个分离株进行了测序并组装了它们的基因组。对所有分离株进行了成对作图和变异调用分析，并检测到少量的分离株间变异。此外，HTS 数据还用于对分离株中的 4029 个 SSR 进行基因分型，仅发现 57 个多态性标记。这些结果证实了该柑橘假单胞菌种群的克隆性。然而，它不是一个完全同质的群体，并且表明 HTS 可以检测到这种精细的遗传分化。两种不同的做法，成对作图和变异调用与 SSR 检测和计算机基因分型，产生了相似的结果，将分离株分为相同的两组。这项研究的结果证明了 HTS 和比较基因组分析在研究这种真菌的遗传多样性和种群结构方面的可行性。