Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises approximately 50% repetitive sequences that include transposable elements. Despite their abundance, two-thirds of TEs remain unclassified, and their regulation among AMF life stages remains unknown. Here, we aimed to improve our understanding of TE diversity and regulation in this model species by curating repeat datasets obtained from chromosome-level assemblies and by investigating their expression across multiple conditions. Our analyses uncovered new TE superfamilies and families in this model symbiont and revealed significant differences in how these sequences evolve both within and between R. irregularis strains. With this curated TE annotation, we also detected that the number of upregulated TE families in colonized roots is four times higher than in the extraradical mycelium, and their overall expression differs depending on the plant host. This work provides a fine-scale view of TE diversity and evolution in model plant symbionts and highlights their transcriptional dynamism and specificity during host-microbe interactions. We also provide Hidden Markov Model profiles of TE domains for future manual curation of uncharacterized sequences (https://github.com/jordana-olive/TE-manual-curation/tree/main).

中文翻译：

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模型植物共生体不规则根噬菌中转座元件的菌株特异性进化和宿主特异性调控

转座元件 (TE) 是重复 DNA，可以产生基因组结构和调控变异。不规则根噬菌是一种广泛研究的丛枝菌根真菌 (AMF)，其基因组包含大约 50% 的重复序列，其中包括转座元件。尽管数量众多，但三分之二的 TE 仍未分类，并且它们在 AMF 生命阶段中的调节作用仍然未知。在这里，我们的目的是通过整理从染色体级组装获得的重复数据集并研究它们在多种条件下的表达，来提高我们对该模型物种中 TE 多样性和调控的理解。我们的分析发现了该模型共生体中新的 TE 超家族和家族，并揭示了这些序列在不规则红线虫菌株内部和之间进化的显着差异。通过这个精心设计的 TE 注释，我们还检测到定植根中上调的 TE 家族数量比自由基外菌丝体高四倍，并且它们的总体表达因植物宿主而异。这项工作提供了模型植物共生体中 TE 多样性和进化的精细视角，并强调了它们在宿主-微生物相互作用过程中的转录活力和特异性。我们还提供 TE 域的隐马尔可夫模型配置文件，以便将来手动管理未表征的序列 (https://github.com/jordana-olive/TE-manual-curation/tree/main)。