Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes
R. Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Daniel Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rüdiger Pukall, James R. White, Neha Varghese, Cody Webb, Krishna Palaniappan, L.C. Reimer, J. Sarda Carbasse, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong‐Yen Wu, Zhiying Zhao, Yu‐Guang Zhou, Lyudmila I. Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe‐Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans‐Peter Klenk, Tanja Woyke, Markus Göker, Nikos C. Kyrpides, Natalia Ivanova
Abstract
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.