Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

中文翻译：

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阿斯加德古细菌的完整基因组揭示了多种整合和移动的遗传元件


Asgard 古细菌作为真核生物的祖先引起了极大的兴趣，但人们对可能影响其持续进化的移动遗传元件 （MGE） 知之甚少。在这里，我们描述了在 Atabeyarchaeia 中复制的 MGE，Atabeyarchaeia 是一个由两个完整基因组表示的湿地 Asgard 古细菌谱系。我们使用土壤深度分辨群体宏基因组数据集来跟踪 18 个 MGE，这些 MGE 定义了基因组结构，并且可以确定精确的染色体整合位点以实现可靠的宿主连锁。此外，我们通过 CRISPR 间隔靶向鉴定了一个完整的 20.67 kbp 环状质粒和两个与 Atabeyarchaeia 相关的家族水平病毒组。密切相关的 40 kbp 病毒具有一个高变基因组区域，编码结构上类似于限制性归巢核酸内切酶的富含半胱氨酸的小蛋白的特定基因组合。一个 10.9 kbp 的整合共轭元件 （ICE） 在基因组上整合到 Atabeyarchaeum deiterrae-1 染色体中，并在其中整合了一个 2.5 kbp 的可循环元件。10.9 kbp ICE 编码表达的 IIG 型限制性修饰系统，其序列特异性与 Pacific Biosciences （PacBio） 高精度长读长 （HiFi） 宏基因组测序鉴定的活性甲基化基序相匹配。Atabeyarchaeia 的限制修饰与另一种共存的 Asgard 古细菌 Freyarchaeia 不同，后者几乎没有已确定的 MGE，但具有不同的防御机制，包括 DISARM 和 Hachiman，这在 Atabeyarchaeia 中没有发现。总体而言，Asgard 古细菌的防御系统和甲基化机制可能调节它们与 MGE 的相互作用，而 MGE 的整合/切除和拷贝数变异反过来又使宿主遗传多功能性成为可能。