ABSTRACT Corynespora cassiicola (Burk. & M.A. Curtis) C.T. Wei. is an anamorphic fungus that affects more than 530 plant species, including economically important crops. Several lineages of this pathogen have been recognized, but the classification of isolates into clades is time-consuming and still sometimes leads to unclear results. In this work, eight major phylogenetic clades (PhL1–PhL8) including 245 isolates of C. cassiicola from 44 plant species were established based on a Bayesian inference analysis of four combined C. cassiicola genomic loci retrieved from GenBank, i.e., rDNA internal transcribed spacer (ITS), actin-1,ga4, and caa5. The existence of PhL1–PhL5 and PhL7 as clonal lineages was further confirmed through the analysis of full-genome single-nucleotide polymorphisms of 39 isolates. Haplotypes of the caa5 locus were PhL specific and encode isoforms of the LDB19 domain of a putative α-arrestin N-terminal–like protein. Evolution of the Caa5 arrestin is in correspondence with the PhLs. ga4 and caa5 PhL consensus sequences and a cleaved amplified polymorphic sequence (CAPS) procedure were generated based on the conserved nucleotide sequences and enzyme restriction patterns observed among isolates from the same lineage, respectively. The CAPS method was validated in silico, and its practical use allowed us to differentiate between tomato and papaya isolates, as well as to reveal the prevalence of PhL1 among isolates infecting soybean in Brazil. This novel approach could be useful in the efforts to control the diseases associated with C. cassiicola.

中文翻译：

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基于 ga4 和 caa5 基因座的核苷酸多态性，一种更新的 Corynespora cassiicola 分离株的系统发育分类和一种实用的鉴定方法

摘要 Corynespora cassiicola (Burk. & MA Curtis) CT Wei。是一种变形真菌，影响 530 多种植物物种，包括具有重要经济意义的作物。这种病原体的几个谱系已经被识别出来，但是将分离株分类为进化枝是耗时的，并且有时仍然会导致不清楚的结果。在这项工作中，基于对从 GenBank 检索到的四个组合 C. cassiicola 基因组位点（即 rDNA 内部转录间隔区）的贝叶斯推理分析，建立了八个主要的系统发育进化枝 (PhL1–PhL8)，包括来自 44 个植物物种的 245 个 C. cassiicola 分离株(ITS)、肌动蛋白-1、ga4 和 caa5。通过对 39 个分离株的全基因组单核苷酸多态性的分析，进一步证实了 PhL1-PhL5 和 PhL7 作为克隆谱系的存在。caa5 基因座的单倍型是 PhL 特异性的，编码推定的 α-抑制蛋白 N 端样蛋白的 LDB19 结构域的同种型。Caa5 抑制蛋白的进化与 PhL 一致。ga4 和 caa5 PhL 共有序列和裂解的扩增多态性序列 (CAPS) 程序是基于保守的核苷酸序列和在同一谱系的分离物中观察到的酶限制模式分别产生的。CAPS 方法在计算机上进行了验证，其实际应用使我们能够区分番茄和木瓜分离株，并揭示了在巴西感染大豆的分离株中 PhL1 的流行情况。这种新方法可能有助于控制与 C. cassiicola 相关的疾病。