Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.
In: Cell genomics, Jg. 2 (2022-12-01), Heft 12
academicJournal
- 100213
Zugriff:
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.
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Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.
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Autor/in / Beteiligte Person: | 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, TBK ; 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 |
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Zeitschrift: | Cell genomics, Jg. 2 (2022-12-01), Heft 12 |
Veröffentlichung: | eScholarship, University of California, 2022 |
Medientyp: | academicJournal |
Umfang: | 100213 |
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