Complete Genome Sequence of Cluster EE Microbacteriophage LaviMo
Lavender Cook, Alyssa Moliis, Anna Josey, Thomas Ray, Ryan Kistemaker, Annica Teasley, Farrah Collins, Alisa Whitcomb, Ryan Swarts, Yazmen Roseboro, Shallah Glover, Ian Goodman, Kaitlyn Dishman, Kimberlyn Pickens, Justin Leonard, D. Parks Collins
Abstract
Microbacteriophage LaviMo is a cluster EE bacteriophage which was isolated from soil collected in Statesville, NC. LaviMo has a 17,453-bp genome with 27 predicted genes, including 3 minor tail genes.
Genome Announcement
Microbacteriophages are viruses which are known to infect microbacterial host species. Microbacteriophage LaviMo was isolated from soil collected from Statesville, NC, USA, by using Microbacterium foliorumNRRL B-24224 SEA. LaviMo was isolated using the direct isolation procedure at 30°C in September 2018. Its plaques were clear. Electron microscopy showed that this bacteriophage has morphology consistent with Siphovirida, a family of double-stranded DNA viruses in the order Caudovirales.
LaviMo plaques were selected, purified, and amplified, and the DNA was extracted. The LaviMo genome was sequenced with the Illumina platform using 3-bp single-end reads and had an average coverage of 5179x. The genome was then annotated using the following databases and software: DNA Master (http://cobamide2.bio.pitt.edu), Glimmer, GeneMark, Starterator, Phamerator, PhagesDB.org, NCBI BLAST and Conserved Domain Database at NCBI, HHPRED, ARAGORN , tRNAscan-SE, and PECAAN (http://pecaan.kbrinsgd.org).
LaviMo is the member of Actinobacteria cluster EE. The LaviMo genome is 17453 bps long, with a 68.9% GC content. After annotation, 25 genes were identified, with 80% of genes being assigned a function. LaviMo was compared to other bacteriophage genomes by using NCBI Blast (https://blast.ncbi.nlm.nih.gov/)and was found to be most similar to bacteriophage Scamander with 99.98% identity and over 97% coverage.
The LaviMo genome is arranged canonically, with the structural genes and viral assembly genes on the leftmost 15 kbp of the genome. At the rightmost 2 kbp of the genome, there are consecutive small reverse genes. A similar arrangement is found in other cluster EE phages. The LaviMo genome has a lysis cassette consisting of lysin A. Between the lysis cassette and immunity cassette there are 3 short reverse genes, which were not found to have any specific functions. Given their position in the genome it is possible that these genes are involved in DNA replication/phage reproduction systems. Other cluster EE bacteriophages such as Scamander have short reverse genes in this position; the number of genes present and the nucleotide sequences are the same for this region. The tape measure protein and minor tail proteins that follow it in Lavimo is identical to that sequence of genes found in the most closely related microbacteriophage, Scamander. The genome also contains the gene MerR-like helix-turn-helix DNA binding protein, which is shared by other cluster EE bacteriophages but is not found in other phage clusters.
When LaviMo was compared to the two cluster phages, it was found that all three genomes obtained a tape measure protein that was located in the same location within the genome. The terminase was also another gene found within all three cluster phages.
Acknowledgments
This work was supported by the Howard Hughes Medical Institute (HHMI) Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program.
We thank Graham F. Hatfull, Welkin H. Pope, Deborah Jacobs-Sera, Daniel A. Russell, and Rebecca A. Garlena for their technical support during the sequencing and annotation of this genome.
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