Genomic Analysis of an Aeromonas hydrophila Phage,Yyong
Objective:Aeromonas hydrophila is a well-known and wide-spread pathogen with increasing drug resistance,posing a threat to fish,livestock,and humans.The aim of this research is to isolate and identify virulent A.hydrophila phages.Methods:Using A.hydrophila Ah2 as an indicator host,the virulent phage Yyong was isolated from sewage using a double-layer agar plate assay.Transmission electron microscopy observation,host range testing,one-step growth experiment,whole genome sequencing,gene annotation,and phylogenetic analysis were performed on it.Results:Yyong is morphologically similar to Myovirus,with a head of(83±2)nm in diameter and a tail(115±5)nm in length.Yyong's genome is 165 663bp in length with a G+C content of 40.90％.Yyong harbors 16 tRNA genes and 242 open reading frame(ORF),including various auxiliary metabolic genes(AMGs)encoding dUTPase,pyrophosphatase MazG,MazG-like pyrophosphatase,NTase,ribonucleotide reductase(RNRs),glutaredoxin(GLRx),thioredoxin(TRX),glutathionylspermidine synthase(GSPS),nicotinamide-nucleotide adenylyltransferase(NMNAT),and nicotinamide phosphoribosyl transferase(NAMPT).The AMGs were mainly involved in DNA synthesis and antioxidant stress.Two ORFs were predicted to encode PAAR repeat protein and DarG antitoxin,which are toxin and antitoxin,respectively,of the toxin-antitoxin(TA)immune system.This may be beneficial for its survival inside bacterial cells.Three ORFs were predicted to encode σ factor,anti-σ70 and host σ70 decoy.They may modify the RNA polymerase to preferentially recognize the promoter region of phage genes rather than host genes,and redirect bacterial energy and resources primarily to phage biosynthesis.In the phylogenetic proteomic tree based on whole-genome comparison,the viruses with the closest evolutionary distance to Yyong are Aeromonas phage T.aes508 and T.aes12 of the Tulanevirus genus.The average nucleotide identity(ANI)value and in silico DNA-DNA hybridization(isDDH)value shared by Yyong and these two phages are 94.06％and 53.30％,and 94.51％,53.00％,respectively,all of which are below the species-defining threshold(ANI＞95％;＞isDDH 70％).Yyong and the phages of the Tulanevirus genus shared the highest whole-genome pairwise sequence comparison(PASC)value and pairwise intergenomic nucleotide sequence identity(VIRIDIC value)of 90.51％and 90.20％,respectively,above the threshold for defining a genus(＞70％).In the phylogenetic proteomic tree,the phages of the Tulanevirus and Biquartavirus genera of the Straboviridae family are grouped into one clade.They share 68.53％of the genes,which meets the criteria of ICTV for establishing a new subfamily(members share 27％～79％of the genes).Conclusions:The results indicate that Yyong reveals a novel species in the Tulanevirus genus.A new subfamily within the Straboviridae family,consisting of the Tulanevirus and Biquartavirus genus,is proposed.The quantity and diversity of AMGs and tRNA genes carried by Yyong enable it to effectively control host bacteria and efficiently synthesize phage-specific nucleic acids and proteins.Some AMGs have potential development value.This research enriches the bacteriophage gene database and the bacteriophage classification system,laying the foundation for the research and development of functional phage genes and phage-based antibiotic alternatives.
NETL
NSTL
万方数据
