Complete Genome Sequence of Rhizobium japonicum Podophage Pasto

Rhizobium japonicum is a Gram-negative bacterium of interest for research into nitrogen fixation in legumes. This article describes the isolation, sequencing, and annotation of R. japonicum podophage Pasto. While it shows no significant similarity to identified phages, genomic analysis indicates that Pasto may be temperate and is a novel T7-like podophage.

R hizobium japonicum is a Gram-negative, motile bacterium with the ability to create a symbiotic relationship with legumes (1), in which the bacterium inhabits root nodules to perform nitrogen fixation (2). R. japonicum phages can be utilized to better understand the bacterial host and possibly to facilitate understanding of the transfer of genetic material in the rhizosphere through transduction (2).
Pasto is a 42,407-bp podophage with a G1C content of 58.6%, which is lower than the average host G1C content of 64.1% (3). Genomic analysis predicted 1 tRNA and 56 protein-coding genes, yielding an overall coding density of 92.8% despite the first 1.0 kb being devoid of coding sequences (CDSs). PhageTerm (18) was used to predict the phage termini, which were identified as 271-bp direct terminal repeats. Thirty-one of the 56 genes were assigned putative functions, of which 12 appear to be similar (BLASTp or BLASTn E values of ,0.001) to those encoded by Escherichia coli phage T7.
This finding suggested that Pasto is a podophage, which was confirmed visually by transmission electron microscopy. Surprisingly, Pasto has many hypothetical proteins that are similar to bacterial proteins, suggesting that it is related to temperate phages despite the prevalence of genes similar to those of T7. A single tRNA gene was found embedded with an antisense orientation within a CDS encoding a hypothetical protein. This tRNA sequence may be a prophage integration site, as previously observed for a mobile genetic element in Rhizobium (19,20).
Data availability. The Pasto genome was deposited in GenBank with accession number MT708545.1. The associated BioProject, SRA, and BioSample accession numbers are PRJNA222858, SRR11558345, and SAMN14609644, respectively.

ACKNOWLEDGMENTS
This work was supported by funding from the National Science Foundation (awards EF-0949351 and DBI-1565146). Additional support came from the CPT, an Initial University Multidisciplinary Research Initiative supported by Texas A&M University and Texas A&M AgriLife Research, and from the Department of Biochemistry and Biophysics of Texas A&M University.
This announcement was prepared in partial fulfillment of the requirements for BICH464 Phage Genomics, an undergraduate course at Texas A&M University.