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.

doi:10.1016/j.xgen.2022.100213

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

Journal Article · Thu Nov 10 23:00:00 EST 2022 · Cell Genomics

DOI:https://doi.org/10.1016/j.xgen.2022.100213· OSTI ID:2475937

^[1]; Roux, Simon ^[1]; Huber, Katharina J. ^[2]; Wu, Dongying ^[1]; Yu, Sora ^[3]; Udwary, Dan ^[4]; Call, Lee ^[1]; Nayfach, Stephen ^[1]; Hahnke, Richard L. ^[2]; Pukall, Rüdiger ^[2]; White, James R. ^[5]; Varghese, Neha J. ^[1]; Webb, Cody ^[1]; Palaniappan, Krishnaveni ^[1]; Reimer, Lorenz C. ^[2]; Sardà, Joaquim ^[2]; Bertsch, Jonathon ^[1]; Mukherjee, Supratim ^[1]; Reddy, T. B.K. ^[1]; Hajek, Patrick P. ^[1] more »

USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Leibniz Inst. DSMZ (Germany)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Resphera Biosciences, Baltimore, MD (United States)
China General Microbiological Culture Collection Center, Beijing (China)
Russian Academy of Sciences (RAS) (Russian Federation)
Hasselt Univ., Diepenbeek (Belgium)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Hokkaido Univ. (Japan)
Univ. of Georgia, Athens, GA (United States)
Newcastle University, Newcastle upon Tyne (United Kingdom)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI)

Grant/Contract Number:: AC02-05CH11231; SC0018260

OSTI ID:: 2475937

Journal Information:: Cell Genomics, Journal Name: Cell Genomics Journal Issue: 12 Vol. 2; ISSN 2666-979X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy Shintani, Masaki; Sanchez, Zoe K.; Kimbara, Kazuhide Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00242	journal	March 2015
Genome-Based Taxonomic Classification of the Phylum Actinobacteria Nouioui, Imen; Carro, Lorena; García-López, Marina Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02007	journal	August 2018
Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis Hu, Dini; Sun, Chenghang; Jin, Tao Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.01540	journal	July 2020
Antimicrobial Peptides: A Potent Alternative to Antibiotics Rima, Mariam; Rima, Mohamad; Fajloun, Ziad Antibiotics, Vol. 10, Issue 9 https://doi.org/10.3390/antibiotics10091095	journal	September 2021
The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Guédon, Gérard; Libante, Virginie; Coluzzi, Charles Genes, Vol. 8, Issue 11 https://doi.org/10.3390/genes8110337	journal	November 2017
Biases in genome reconstruction from metagenomic data Nelson, William C.; Tully, Benjamin J.; Mobberley, Jennifer M. PeerJ, Vol. 8 https://doi.org/10.7717/peerj.10119	journal	January 2020

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59 BASIC BIOLOGICAL SCIENCES
actinobacteria
comparative genomics
ecology
evolution
metagenomics
microbiology
mycobacteria
secondary metabolites

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

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