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Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.
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.
Affiliation
  • Seshadri R; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Roux S; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Huber KJ; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  • Wu D; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Yu S; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Udwary D; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Call L; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Nayfach S; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Hahnke RL; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Pukall R; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  • White JR; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  • Varghese NJ; Resphera Biosciences, Baltimore, MD, USA.
  • Webb C; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Palaniappan K; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Reimer LC; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Sardà J; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  • Bertsch J; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  • Mukherjee S; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Reddy TBK; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Hajek PP; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Huntemann M; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Chen IA; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Spunde A; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Clum A; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Shapiro N; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Wu ZY; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Zhao Z; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Zhou Y; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Evtushenko L; China General Microbiological Culture Collection Center, Beijing, China.
  • Thijs S; Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, All-Russian Collection of Microorganisms (VKM), Pushchino, Russia.
  • Stevens V; Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium.
  • Eloe-Fadrosh EA; Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium.
  • Mouncey NJ; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Yoshikuni Y; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Whitman WB; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Klenk HP; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Woyke T; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.
  • Göker M; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Kyrpides NC; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Ivanova NN; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Cell Genom ; 2(12): 100213, 2022 Dec 14.
Article in En | MEDLINE | ID: mdl-36778052
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Cell Genom Year: 2022 Document type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Cell Genom Year: 2022 Document type: Article Affiliation country: United States