Joris A Alkemade, Pierre Hohmann, Monika M Messmer, Timothy G Barraclough
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Phylogenomics confirmed the presence of four distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), and deletions revealed that lineage II could be split into two groups, II-A and II-B. TE content varied between lineages and correlated strongly with genome size variation, supporting a role for TEs in genome expansion in this species. Pangenome analysis revealed a highly variable accessory genome, including a minichromosome present in lineages II, III, and IV, but absent in lineage I. Accessory genes and effectors appeared to cluster in proximity to TEs. Presence/absence variation of putative effectors was lineage-specific, suggesting that these genes play a crucial role in determining host range. Notably, no effectors were found on the TE-rich minichromosome. 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Our findings shed light on the potential mechanisms generating genetic diversity in this asexual fungal pathogen that could aid future disease management.</p>\",\"PeriodicalId\":18763,\"journal\":{\"name\":\"Molecular plant pathology\",\"volume\":\"25 12\",\"pages\":\"e70039\"},\"PeriodicalIF\":4.8000,\"publicationDate\":\"2024-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645255/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular plant pathology\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1111/mpp.70039\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular plant pathology","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1111/mpp.70039","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
摘要
植物真菌病原体在全球范围内给农作物造成了重大损失,其中许多病原体的基因组具有区隔性,包括核心区和附属区,这被认为是适应性的驱动因素。对寄主具有高度特异性的 Colletotrichum lupini 真菌极大地影响了羽扇豆(羽扇豆属)的种植。这种病原体属于 C. acutatum 物种复合体第 1 支系,由四个基因一致、可能是克隆的支系(I-IV)组成。尽管如此,在这些品系中仍可观察到毒力和形态上的变异。为了研究这种无性真菌遗传变异的潜在来源,我们比较了 16 个 C. lupini 菌株和 17 个相关 Colletotrichum 物种的基因组。系统发生组学证实存在四个不同的品系,但基于基因组大小、基因含量、转座元件(TE)和缺失的进一步研究发现,品系 II 可分为两组,即 II-A 和 II-B。TE含量在不同品系之间存在差异,并且与基因组大小的变化密切相关,这支持了TE在该物种基因组扩增中的作用。Pangenome 分析表明,附属基因组变化很大,包括在品系 II、III 和 IV 中出现的迷你染色体,但在品系 I 中却不存在。假定效应因子的存在/不存在差异具有品系特异性,这表明这些基因在决定宿主范围方面起着至关重要的作用。值得注意的是,在富含TE的小染色体上没有发现效应基因。我们的发现揭示了这种无性真菌病原体产生遗传多样性的潜在机制,有助于未来的疾病管理。
Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini.
Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host-specific fungus Colletotrichum lupini greatly impacts lupin (Lupinus spp.) cultivation. This pathogen is part of clade 1 of the C. acutatum species complex and comprises four genetically uniform, presumably clonal, lineages (I-IV). Despite this, variation in virulence and morphology has been observed within these lineages. To investigate the potential sources of genetic variability in this asexual fungus, we compared the genomes of 16 C. lupini strains and 17 related Colletotrichum species. Phylogenomics confirmed the presence of four distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), and deletions revealed that lineage II could be split into two groups, II-A and II-B. TE content varied between lineages and correlated strongly with genome size variation, supporting a role for TEs in genome expansion in this species. Pangenome analysis revealed a highly variable accessory genome, including a minichromosome present in lineages II, III, and IV, but absent in lineage I. Accessory genes and effectors appeared to cluster in proximity to TEs. Presence/absence variation of putative effectors was lineage-specific, suggesting that these genes play a crucial role in determining host range. Notably, no effectors were found on the TE-rich minichromosome. Our findings shed light on the potential mechanisms generating genetic diversity in this asexual fungal pathogen that could aid future disease management.
期刊介绍:
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