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This release (MAGs v2) is a major new version of this metagenome-assembled genome (MAG) set. All previous releases on this page (which only differ in the metadata) are designated "MAGs v1." The current release (MAGs v2) uses CheckM2 v1.0.2 filtering (≥70% completeness, ≤10% contamination) to expand this dataset to include 36,419 MAGs, with the following subcategories: Cronin_v1:  Manually-curated subset of the "Field" category from MAGs v1. Cronin_v2:  MAGs from raw bin filtering on the same assemblies used to generate Cronin_v1. Woodcroft_v2:  MAGs from raw bin filtering on the same assemblies used to generate the MAGs reported in Woodcroft & Singleton et al. (2018). SIPS:  Updated genomes from samples originating from a stable isotope probing (SIP) incubation experiment by Moira Hough et al. ("SIP" in MAGs v1), re-analyzed due to read truncation and sample linkage issues in MAGs v1. JGI:  Expanded set of genomes from the Joint Genome Institute's metagenome annotation pipeline.   FILES: Emerge_MAGs_v2.tar.gz - Archive containing the MAG files (.fna). metadata_MAGs_v2_EMERGE.tsv - Table containing source sample names and accessions, GTDB taxonomy information, CheckM2 quality reports, NCBI GenomeBatch- and MIMAG(6.0)-formatted sample attributes and other metadata for the MAGs.    FUNDING: This research is a contribution of the EMERGE Biology Integration Institute (https://emerge-bii.github.io/), funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070. This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632. DE-SC0010580. and DE-SC0016440. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. Data collected at the Joint Genome Institute was generated under the following awards: The majority of sequencing at JGI was supported by BER Support Science Proposal 503530 (DOI: 10.46936/10.25585/60001148), conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Sequencing of SIP samples was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative (proposal 503547; award DOI: 10.46936/fics.proj.2017.49950/60006215) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Office of Biological and Environmental Research and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). 

Abstract Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.