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Title: | Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes | Authors: | Seshadri, Rekha Roux, Simon Huber, Katharina J. Wu, Dongying Yu, Sora Udwary, Dan Call, Lee Nayfach, Stephen Hahnke, Richard L. Pukall, Rüdiger White, James R. Varghese, Neha J. Webb, Cody Palaniappan, Krishnaveni Reimer, Lorenz C. Sardà, Joaquim Bertsch, Jonathon Mukherjee, Supratim Reddy, T.B.K. Hajek, Patrick P. Huntemann, Marcel Chen, I-Min A. Spunde, Alex Clum, Alicia Shapiro, Nicole Wu, Zong-Yen Zhao, Zhiying Zhou, Yuguang Evtushenko, Lyudmila THIJS, Sofie STEVENS, Vincent Eloe-Fadrosh, Emiley A. Mouncey, Nigel J. Yoshikuni, Yasuo Whitman, William B. Klenk, Hans-Peter Woyke, Tanja Göker, Markus Kyrpides, Nikos C. Ivanova, Natalia N. |
Issue Date: | 2022 | Publisher: | Source: | Cell Genomics, (Art N° 100213) | Abstract: | The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. | Document URI: | http://hdl.handle.net/1942/38976 | e-ISSN: | 2666-979X | DOI: | 10.1016/j.xgen.2022.100213 | Rights: | 2022 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). | Category: | A1 | Type: | Journal Contribution | Validations: | vabb 2024 |
Appears in Collections: | Research publications |
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