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. 2022 Jun 22;607(7917):111–118. doi: 10.1038/s41586-022-04862-3

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 6 — (a, c–f) Anvi'o interface of representatives of the five Ca. Eudoremicrobiaceae species reveals stable abundance correlation patterns across the vast majority of the genomes, indicative of low contamination rates (Supplementary Information). (b) Inspection of the assembly graph for Ca. E. malaspinii (Supplementary Information) showed that all scaffolds from the representative genomes were connected with the exception of a single 20 kb one. (g) Investigating the evolutionary history of duplicated single-copy marker genes (here COG0124), we found consistent duplication across Ca. Eudoremicrobeaceae and the parent order UBP9, thus ruling out the duplication as a signal of contamination in the binning process. The different evolutionary history of the second copy of COG0124 (right-hand side of the tree), with closer relationship to Actinobacteria suggests that introgression events (including before the UBP9 and Ca. Eudoremicrobiaceae split) could be the origin of the increased genome size and biosynthetic potential observed in Ca. Eudoremicrobiaceae. (h) Similar patterns can be found in the second duplicated marker gene (COG0522), although duplication was not detected across all Ca. Eudoremicrobeaceae spp. representatives.