Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization.

IF 2.4 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Chromosome Research Pub Date : 2021-06-01 Epub Date: 2021-05-21 DOI:10.1007/s10577-021-09658-1
Jessica L Soyer, Colin Clairet, Elise J Gay, Nicolas Lapalu, Thierry Rouxel, Eva H Stukenbrock, Isabelle Fudal
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引用次数: 6

Abstract

Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.

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两种黄斑钩端绦虫在无性系生长过程中组蛋白修饰的全基因组图谱显示了不同的基因组组织。
maculans Leptosphaeria 'brassicae' (Lmb)和lepidii' Leptosphaeria maculans 'lepidii' (Lml)是密切相关的植物致病物种,它们表现出大的宏观同质性,但基因组结构不同。Lmb有超过30%的重复序列聚集在重复序列丰富的大区域,而Lml基因组只有少量均匀分布的重复序列。Lmb的重复区富含效应基因,在植物侵染过程中表达。Lmb和Lml不同的基因组结构为比较两种密切相关的植物病原真菌中与染色质景观相关的致病性基因组织提供了一个很好的模型。在这里,我们在无菌培养期间进行了染色质免疫沉淀(ChIP),针对异染色质或常染色质的典型组蛋白修饰,结合转录组学分析来分析染色质组织对基因表达的影响。在这两个物种中,我们发现兼性异染色质富含缺乏功能注释的基因,包括许多效应基因和物种特异性基因。值得注意的是,位于H3K27me3结构域的同源基因富含效应基因。与其他真菌物种(包括Lml)相比,Lmb的独特之处是具有与含有许多物种特异性效应基因的重复序列丰富区域相关的大H3K9me3结构域。这两种不同的异染色质景观的发现现在提出了关于它们参与致病性调节的问题,植物感染期间这些结构域的动态以及真菌在H3K9me3或H3K27me3结构域中宿主效应基因的选择优势。
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来源期刊
Chromosome Research
Chromosome Research 生物-生化与分子生物学
CiteScore
4.70
自引率
3.80%
发文量
31
审稿时长
1 months
期刊介绍: Chromosome Research publishes manuscripts from work based on all organisms and encourages submissions in the following areas including, but not limited, to: · Chromosomes and their linkage to diseases; · Chromosome organization within the nucleus; · Chromatin biology (transcription, non-coding RNA, etc); · Chromosome structure, function and mechanics; · Chromosome and DNA repair; · Epigenetic chromosomal functions (centromeres, telomeres, replication, imprinting, dosage compensation, sex determination, chromosome remodeling); · Architectural/epigenomic organization of the genome; · Functional annotation of the genome; · Functional and comparative genomics in plants and animals; · Karyology studies that help resolve difficult taxonomic problems or that provide clues to fundamental mechanisms of genome and karyotype evolution in plants and animals; · Mitosis and Meiosis; · Cancer cytogenomics.
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