Thousands of small, novel genes predicted in global phage genomes

Fremin, Brayon J., Bhatt, Ami S. and Kyrpides, Nikos C. and Global Phage Small Open Reading Frame (GP-SmORF) Consortium (2022) Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39 (12). ISSN 2211-1247

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Abstract

Small genes (<150 nucleotides) 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 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families 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.

Item Type:	Article
Additional Information:	Funding Information: The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Computing costs were also supported via NIH S10 Shared Instrumentation Grant (1S10OD02014101), NIH R01 #AI148623–01, A Sloan Foundation Fellowship, and Damon Runyon Clinical Investigator Award to A.S.B. Sample collection costs were supported by NSF grants 1826734 and 1441717 as well as Simons Foundation grant 827839.
Uncontrolled Keywords:	cp: microbiology,metaribo-seq,comparative genomics,gene families,microbiome,phage,sorfs,small genes,biochemistry, genetics and molecular biology(all) ,/dk/atira/pure/subjectarea/asjc/1300
Faculty \ School:	Faculty of Science > School of Environmental Sciences University of East Anglia Research Groups/Centres > Theme - ClimateUEA
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences Faculty of Science > Research Groups > Environmental Biology
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	11 Mar 2024 09:32
Last Modified:	18 Mar 2024 09:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/94614
DOI:	10.1016/j.celrep.2022.110984

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