Thousands of small, novel genes predicted in global phage genomes

Fremin, Brayon; Bhatt, Ami; Kyrpides, Nikos; GP-SmORF, Consortium; Ward, Nicholas D.; Stegen, James C.

doi:10.1016/j.celrep.2022.110984

Thousands of small, novel genes predicted in global phage genomes

Journal Article · Tue Jun 21 04:00:00 EDT 2022 · Cell Reports

DOI:https://doi.org/10.1016/j.celrep.2022.110984· OSTI ID:2565839

Fremin, Brayon ^[1]; Bhatt, Ami ^[2]; Kyrpides, Nikos ^[3]; GP-SmORF, Consortium ^[4]; ^[5]; ^[5]

Lawrence Berkeley National Laboratory
Stanford University
Joint Genome Institute
Multiple Institutions
BATTELLE (PACIFIC NW LAB)

Small genes (<150nucleotides) have been systematically overlooked in phage genomes. We employ a large scale comparative genomics approach to predict >40,000 small-gene families in 2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000families encode predicted anti-CRISPR proteins, and more than500families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 2565839

Report Number(s):: PNNL-SA-171375

Journal Information:: Cell Reports, Journal Name: Cell Reports Journal Issue: 12 Vol. 39

Country of Publication:: United States

Language:: English

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