Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
PLoS Genetics Pub Date : 2024-10-25 eCollection Date: 2024-10-01 DOI:10.1371/journal.pgen.1011452
Petros Skiadas, Sofía Riera Vidal, Joris Dommisse, Melanie N Mendel, Joyce Elberse, Guido Van den Ackerveken, Ronnie de Jonge, Michael F Seidl
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引用次数: 0

Abstract

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.

庞基因组图谱分析揭示了菠菜霜霉病中广泛的效应因子拷贝数变异。
植物病原体的适应速度对当代病害管理策略(如抗病基因的部署)提出了挑战。适应的强大进化压力塑造了病原体的基因组,而比较基因组学在描述这一过程中发挥了重要作用。为了高分辨率地捕捉基因组变异并研究导致适应的过程,我们在此利用创新的多基因组方法构建并注释了第一个卵菌植物病原体的泛基因组图谱。我们通过分析该图并为所有基因创建基于同源关系的单拷贝正交群来扩展这种方法。我们对卵菌病原 Peronospora effusa 的六个不同基因的分离株进行了端粒到端粒的基因组组装,Peronospora effusa 是全球栽培菠菜中经济上最重要的病害。基因组图谱表明,P. effusa 的基因组在染色体结构和基因内容方面都高度保守,并揭示了转座元件的持续活动,这些转座元件是造成分离株之间观察到的变异的 80% 的直接原因。虽然大多数基因总体上是保守的,但与毒力相关的基因在不同分离物之间的变异很大。大部分变异出现在因大量拷贝数扩增而形成的大型基因簇中。因此,基于庞基因组图谱的发现可以有效地用于捕捉分辨率极高的基因组变异,从而为研究植物病原体的生物学和进化提供一个框架。
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来源期刊
PLoS Genetics
PLoS Genetics GENETICS & HEREDITY-
自引率
2.20%
发文量
438
期刊介绍: PLOS Genetics is run by an international Editorial Board, headed by the Editors-in-Chief, Greg Barsh (HudsonAlpha Institute of Biotechnology, and Stanford University School of Medicine) and Greg Copenhaver (The University of North Carolina at Chapel Hill). Articles published in PLOS Genetics are archived in PubMed Central and cited in PubMed.
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