Genomics, evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes
Genomics, evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes
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链格孢属物种组（包括苹果和亚洲梨致病型）的基因组学、进化史和诊断
DOI：
10.1101/534685
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Armitage A
中科院分区：
文献类型：
--
作者：
Armitage A
alternariasectionalternnaria （alternnaria alternatspecies group）代表了腐殖质、人类过敏原和植物病原体的一个多样化群体。交替分类学受益于最近的系统发育修订，但在该群体内主要系统发育分支之间的区分基础尚不清楚。此外，用于研究宿主特异性致病型的基因组资源有限。我们报告了苹果和亚洲梨病型的近完整基因组，以及另外10个代表tenuishimia和arborescencenia谱系的分离株的草图组装。这些组合提供了对这些分类群的分化的第一个见解，并允许描述苹果和梨的有条件可有可无染色体（CDCs）的效应和非效应谱。我们确定了本研究中测序的分离株与另外23个alternariaspp的系统发育关系。基于可用的基因组。我们确定哪些基因组代表MAT1-1-1或MAT1-2-1自形态，并指定宿主特异性病理类型。我们首次表明苹果的致病型是多系的，存在于两个theA中。arborescensandA。tenuissimalineages。此外，我们分析了89个更广泛的菌株，用于交配型自形和毒素基因标记。交配型分布表明，自a形成以来就发生了基因流动。tenuissimaandA。arborescenslineages。我们还开发了amt14的引物，amt14是苹果致病毒素基因簇的一个基因，在所有被测试的致病类型中都有同源物。这些引物可用于苹果、梨、草莓等病原菌的鉴定和鉴别，为病原菌诊断提供了新的工具。
TheAlternariasectionalternaria(Alternaria alternataspecies group) represents a diverse group of saprotroph, human allergens, and plant pathogens.Alternariataxonomy 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 representingAlternaria tenuissimaandAlternaria arborescenslineages. 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 23Alternariaspp. 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 theA. arborescensandA. tenuissimalineages. 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 ofA. tenuissimaandA. arborescenslineages. We also developed primers designed toAMT14, 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.