Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands.
Laboratory of Genetics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands.
BMC Genomics. 2023 Jan 28;24(1):53. doi: 10.1186/s12864-023-09126-6.
Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.
Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.
Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.
丛枝菌根（AM）真菌可以说是植物最重要的共生体，为其宿主提供了一系列益处。然而，这些益处的提供似乎并不均匀，真菌共生体之间的遗传变异对植物的表现有很大的影响。有趣的是，真菌个体内部也存在遗传变异，这些个体包含数百万个共享细胞质的单倍体核。在模式 AM 真菌，粗糙脉孢菌中，已经报道了几个分离株是双核体，含有两种遗传上不同类型的核，基于其交配型（MAT）基因座的身份来识别。然而，它们极度的原生质团性质和缺乏已知的单个核阶段，引发了关于这种遗传变异的起源、分布和动态的问题。
在这里，我们在菌丝个体、单个孢子和单个核水平上进行了 DNA 和 RNA 测序，以深入了解类似于双核体的粗糙脉孢菌 C3 分离株的动态遗传结构，以及不同宿主植物对其遗传变异的影响。我们的分析表明，在 C3 中，平行的孢子和根培养批次中可以有两种主要基因型的广泛变化比例。此外，还发现了许多多态性，其频率与一般基因型比例显著偏离，表明存在多样化的略有不同核型的种群。在多次传代后，改变宿主植物并没有显示出对核型比例的一致宿主效应。相反，我们发现了宿主植物身份对 C3 中等位基因特异性表达的主要影响。
我们的分析表明，粗糙脉孢菌的不同分离株中存在高度动态/可变的遗传组织。在孢子形成时核型比例似乎随机波动、重组事件、非串联重复 rDNA 序列的高度变异性以及依赖宿主的等位基因表达，所有这些都增加了变异水平，可能有助于这些广泛共生体的进化成功。
