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Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang, Katelyn McNair, Daniel A. Cuevas, Barbara A. Bailey, Anca M. Segall, View ORCID ProfileRobert A. Edwards
doi: https://doi.org/10.1101/114819
Han Suh Kang
1Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Katelyn McNair
2Department of Computer Science, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Daniel A. Cuevas
3Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Barbara A. Bailey
4Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Anca M. Segall
1Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Robert A. Edwards
1Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
2Department of Computer Science, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
3Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182
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Abstract

Temperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the host’s genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts’ translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 07, 2017.
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Prophage genomics reveals patterns in phage genome organization and replication
Han Suh Kang, Katelyn McNair, Daniel A. Cuevas, Barbara A. Bailey, Anca M. Segall, Robert A. Edwards
bioRxiv 114819; doi: https://doi.org/10.1101/114819
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Prophage genomics reveals patterns in phage genome organization and replication
Han Suh Kang, Katelyn McNair, Daniel A. Cuevas, Barbara A. Bailey, Anca M. Segall, Robert A. Edwards
bioRxiv 114819; doi: https://doi.org/10.1101/114819

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