Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado1,2,
- Ling-Dong Shi1,
- Kathryn E. Appler3,
- Alexander Crits-Christoph1,2,11,
- Valerie De Anda3,4,
- Benjamin A. Adler1,
- Michael L. Cui1,
- Lynn Ly5,
- Pedro Leão3,12,
- Richard J. Roberts6,
- Rohan Sachdeva1,
- Brett J. Baker3,4,
- David F. Savage1,7,8 and
- Jillian F. Banfield1,4,9,10
- 1Innovative Genomics Institute, University of California, Berkeley, California 94720, USA;
- 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
- 3Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas 78373, USA;
- 4Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
- 5Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA;
- 6New England Biolabs, Ipswich, Massachusetts 01938, USA;
- 7Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA;
- 8Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA;
- 9Earth and Planetary Science, University of California, Berkeley, California 94720, USA;
- 10Department of Microbiology, Biomedicine Discovery Institute, Monash University, Victoria 3168, Australia
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279480.124.
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Freely available online through the Genome Research Open Access option.
- Received April 17, 2024.
- Accepted August 27, 2024.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
