The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.

中文翻译：

---

基因组进化史和诊断的交替链孢菌种组，包括苹果和亚洲梨病原体。

链格孢属（Alternaria alternata物种组）代表了腐生菌，人类变应原和植物病原体的不同种类。交链孢菌分类学得益于最近的系统进化研究，但该组内主要系统进化分支之间的区分基础尚不清楚。此外，用于研究宿主特异性病理型的基因组资源有限。我们报道了苹果和亚洲梨致病型的近完整基因组，以及代表另外的10个分离株（代表链格孢和链格孢）的分离株的草图。这些程序集提供了对这些分类群分化的初步见解，并允许描述苹果和梨有条件可分配染色体（CDC）的效应子和非效应子谱。我们定义了在这项研究中测序的菌株与另外23种链格孢菌之间的系统发育关系。基于可用的基因组。我们确定这些基因组中的哪些代表MAT1-1-1或MAT1-2-1独特型，并指定宿主特异性病理型。我们首次显示苹果病原体是多系的，存在于侧柏木和tenuissima谱系中。此外，我们针对交配型独特型和毒素基因标记物对89个分离株进行了更广泛的分析。交配型分布表明，自tenuissima和Aborescens谱系形成以来已经发生了基因流动。我们还开发了针对AMT14设计的引物，AMT14是苹果病原体毒素基因簇中的一个基因，在所有测试的病原体中均具有同源性。这些引物可以鉴定和区分苹果，梨，