Cell Genomics
Volume 2, Issue 12, 14 December 2022, 100213
Journal home page for Cell Genomics

Article
Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

https://doi.org/10.1016/j.xgen.2022.100213Get rights and content
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Highlights

  • 824 new actinobacterial isolate genomes from diverse environments

  • Only a third of actinobacterial diversity has genome representation

  • New niche-specific gene determinants highlighted, such as new antimicrobial peptides

  • Secondary metabolite gene clusters shaped by horizontal gene transfer

Summary

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.

Keywords

microbiology
comparative genomics
secondary metabolites
actinobacteria
metagenomics
ecology
evolution
mycobacteria

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