Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and B. kuwatsukai. Here, we sequenced the genomes of B. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and B. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g. carbohydrate active enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in B. dothidea and B. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.

中文翻译：

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苹果环腐病的致病菌 Botryosphaeria dothidea 和 B. kuwatsukai 的比较基因组学揭示了致病性相关基因的物种扩展和物种形成过程中毒力基因含量的变化。

环腐病是全世界苹果最具破坏性的病害之一，主要由 Botryosphaeria dothidea 和 B. kuwatsukai 引起。在这里，我们对 B. dothidea 菌株 PG45（44.3 Mb，重复率 5.12%）和 B. kuwatsukai 表型菌株 PG2（48.0 Mb，重复率 13.02%）进行了基因组测序，并对这两个基因组进行了比较分析。与其他测序的真菌基因组一样，为了了解致病性相关基因的物种形成和独特的进化模式。配对基因组比对显示，这两个物种具有高度同线性（平均序列同一性为 96.74%）。相比之下，这两个物种都编码大量致病性相关基因，例如碳水化合物活性酶（CAZY）、植物细胞壁降解酶（PCWDE）、次生代谢物（SM）生物合成酶、细胞色素P450酶（CYP）和分泌肽酶涉及各种生活方式的所有其他已测序真菌物种。B. dothidea 和 B. kuwatsukai 中致病性相关基因的数量高于 Botryosphaeriaceae 病原体（Macrophomina Phaseolina 和 Neofusicoccum parvum）的其他基因组，表明该科存在第二轮 Botryosphaeria 谱系扩张。然而，这两个葡萄球菌属物种的基因组也存在显着差异。仅感染苹果和梨的 Botryosphaeria kuwatsukai 显然丢失了一组 SM 基因、CAZY 和 PCWDE，这可能是宿主特化的结果。Botryosphaeria kuwatsukai 比 B. dothidea 含有更多的转座因子和更高的重复诱导点 (RIP) 指数。我们的结果将有助于了解这两种植物病原体如何与其植物宿主相互作用，并有助于设计有效的疾病控制和分子育种策略，以帮助确保全球苹果生产和粮食安全。