{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T07:28:49Z","timestamp":1774078129776,"version":"3.50.1"},"posted":{"date-parts":[[2026,3,20]]},"group-title":"Microbiology","reference-count":0,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:00:00Z","timestamp":1773964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,20]]},"abstract":"<jats:p>It has been known for decades that bacteriophages encode tRNA genes, but their function and the factors contributing to their acquisition and retention are unclear. Although tRNAs are found in a variety of phages infecting a variety of bacteria, many large-scale computational studies investigating tRNA acquisition and retention in phages are specific to Mycobacterium phages; however, these findings may not be representative of other phages or bacteria. This work uses a broader sampling of phages and hosts to investigate the relationships between codon usage bias, infection cycle, and tRNA gene numbers in phage genomes. We analyzed 154 phages infecting 7 host genera, including Gram-negative (Escherichia, Shigella, Salmonella) and Gram-positive (Bacillus, Lactobacillus, Staphylococcus, Mycobacterium) bacteria. Phages included temperate and virulent representatives, plus a range of tRNA numbers and morphologies. All phages and hosts were analyzed using four metrics: GC content, Effective Number of Codons, Relative Synonymous Codon Usage, and tRNA Adaptation Index. On a global scale, virulent phages with many tRNA genes show greater differences in codon usage and codon adaptation compared to their respective hosts. Gram-negative bacteria and their phages generally exhibit greater differences in codon usage compared to Gram-positive bacteria and their phages. Phages infecting Gram-negative hosts also tend to encode more tRNA genes. In nearly all genus-level comparisons, Mycobacterium phages were different from any other host and from global patterns. This suggests previous computational studies performed in Mycobacterium phages are likely not applicable on a global scale or to phages infecting other host genera.<\/jats:p>","DOI":"10.64898\/2026.03.19.712862","type":"posted-content","created":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T04:20:11Z","timestamp":1774066811000},"source":"Crossref","is-referenced-by-count":0,"title":["A comprehensive computational analysis investigating the relationships between phage codon usage, infection style, and number of tRNA genes"],"prefix":"10.64898","author":[{"given":"Nykki D","family":"Ross","sequence":"first","affiliation":[{"name":"University of Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7672-2355","authenticated-orcid":false,"given":"Sarah M.","family":"Doore","sequence":"additional","affiliation":[{"name":"University of Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.03.19.712862","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T04:20:11Z","timestamp":1774066811000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.03.19.712862"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,20]]},"references-count":0,"URL":"https:\/\/doi.org\/10.64898\/2026.03.19.712862","relation":{},"subject":[],"published":{"date-parts":[[2026,3,20]]},"subtype":"preprint"}}