BACKGROUND Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. RESULTS We also sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea using Nanopore MinION sequencing for additional comparative analyses within the Alternaria genus. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. CONCLUSION The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.

中文翻译：

---

链格孢菌属物种的比较基因组学提供了对十字格孢菌（十字花科病原体）的致病生活方式的见解。

背景技术 芸苔链格孢(Alternaria brasicae)，一种坏死营养型病原体，引起链格孢叶斑病，其是芸苔属作物的重要经济病害之一。许多其他链格孢属属。已知诸如A.Brassicicola和A.alternata之类的A.brassicicola和A.alternata会在受A.brassicae感染的芸苔属植物中引起继发性感染。甘蓝菜的基因组结构、致病因素和宿主特异性的决定因素尚不清楚。在这项研究中，我们对最近公布的芸苔菌基因组组装进行了注释和表征，并将其与其他链格孢属进行了比较。深入了解其致病生活方式。结果我们还使用 Nanopore MinION 测序对共同感染芥菜的两种链格孢 A. alternata 分离株进行了基因组测序，以在链格孢属内进行额外的比较分析。链格孢属 (Alternaria spp) 内的基因组比对。揭示了大多数染色体之间存在高水平的同线性，并伴有一些染色体内重排。我们首次证明，大孢子链格孢属（Alternaria）物种的基因组中含有一条可有可无的染色体。我们鉴定了 460 个甘蓝菜特异性基因，其中包括许多分泌蛋白和效应子。此外，我们还鉴定了负责产生 Destruxin-B（甘蓝菜已知的致病因子）的基因簇。结论 这项研究为了解链格孢属内独特且共有的基因库提供了视角，并确定了可能导致芸苔链格孢致病生活方式的基因。