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Complete genome sequence of Paracoccus marcusii phage vB_PmaS-R3 isolated from the South China Sea.

Xu Y, Zhang R, Jiao N - Stand Genomic Sci (2015)

Bottom Line: In addition, four gene transfer agent-like genes were found in the vB_PmaS-R3 genome.A putative L-alanoyl-D-glutamate peptidase was predicted as the endolysin.A MazG gene was found in the vB_PmaS-R3 genome, which indicates genomic adaption to the nutrient-limited marine environment.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.

ABSTRACT
Paracoccus spp. are isolated from both terrestrial and aquatic habitats, indicating their ubiquitous existence in the environment. Here we present the first phage isolated from this genus, vB_PmaS-R3, and its complete genome sequence. Paracoccus phage vB_PmaS-R3 is a siphophage isolated from the South China Sea. The genome sequence is 42,093 bp, with a G + C content of 56.36 %. Fifty-two open reading frames were predicted from the genome. The genome can mainly be divided into three regions: genes for DNA metabolism, regulatory genes and structure forming genes. Genes encoding DNA metabolism and structural proteins showed high sequence homology to corresponding genes of Burkholderia phage KL1 and Pseudomonas phage PA73. In addition, four gene transfer agent-like genes were found in the vB_PmaS-R3 genome. A putative L-alanoyl-D-glutamate peptidase was predicted as the endolysin. A MazG gene was found in the vB_PmaS-R3 genome, which indicates genomic adaption to the nutrient-limited marine environment.

No MeSH data available.


Genome map of Paracoccus phage vB_PmaS-R3 and comparative genomic analysis with Burkholderia phage KL1 and Pseudomonas phage PA73
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Fig3: Genome map of Paracoccus phage vB_PmaS-R3 and comparative genomic analysis with Burkholderia phage KL1 and Pseudomonas phage PA73

Mentions: The properties and statistics of the genome are summarized in Tables 3 and 4. Phage vB_PmaS-R3 has a circular double-stranded DNA genome with a length of 42,093 bp and a G + C content of 56.37 % (Table 3). Fifty-two ORFs were predicted from the genome with a coding efficiency of 92.79 %. Among the 52 ORFs, 11 had no matches in the NCBI non-redundant protein database, 33 were homologous to genes identified in phages, while seven were only found in bacteria. Strikingly, one (ORF30) was found to be closely related to a gene identified from an algal virus, Dunaliella viridis virus SI2 (Additional file 1: Table S1). Of the 44 ORFs that have matches in the NCBI database, 28 were assigned to putative functions (Fig. 3, Additional file 1: Table S1). The distribution of genes into COG categories is presented in Table 4.Table 3


Complete genome sequence of Paracoccus marcusii phage vB_PmaS-R3 isolated from the South China Sea.

Xu Y, Zhang R, Jiao N - Stand Genomic Sci (2015)

Genome map of Paracoccus phage vB_PmaS-R3 and comparative genomic analysis with Burkholderia phage KL1 and Pseudomonas phage PA73
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4641407&req=5

Fig3: Genome map of Paracoccus phage vB_PmaS-R3 and comparative genomic analysis with Burkholderia phage KL1 and Pseudomonas phage PA73
Mentions: The properties and statistics of the genome are summarized in Tables 3 and 4. Phage vB_PmaS-R3 has a circular double-stranded DNA genome with a length of 42,093 bp and a G + C content of 56.37 % (Table 3). Fifty-two ORFs were predicted from the genome with a coding efficiency of 92.79 %. Among the 52 ORFs, 11 had no matches in the NCBI non-redundant protein database, 33 were homologous to genes identified in phages, while seven were only found in bacteria. Strikingly, one (ORF30) was found to be closely related to a gene identified from an algal virus, Dunaliella viridis virus SI2 (Additional file 1: Table S1). Of the 44 ORFs that have matches in the NCBI database, 28 were assigned to putative functions (Fig. 3, Additional file 1: Table S1). The distribution of genes into COG categories is presented in Table 4.Table 3

Bottom Line: In addition, four gene transfer agent-like genes were found in the vB_PmaS-R3 genome.A putative L-alanoyl-D-glutamate peptidase was predicted as the endolysin.A MazG gene was found in the vB_PmaS-R3 genome, which indicates genomic adaption to the nutrient-limited marine environment.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.

ABSTRACT
Paracoccus spp. are isolated from both terrestrial and aquatic habitats, indicating their ubiquitous existence in the environment. Here we present the first phage isolated from this genus, vB_PmaS-R3, and its complete genome sequence. Paracoccus phage vB_PmaS-R3 is a siphophage isolated from the South China Sea. The genome sequence is 42,093 bp, with a G + C content of 56.36 %. Fifty-two open reading frames were predicted from the genome. The genome can mainly be divided into three regions: genes for DNA metabolism, regulatory genes and structure forming genes. Genes encoding DNA metabolism and structural proteins showed high sequence homology to corresponding genes of Burkholderia phage KL1 and Pseudomonas phage PA73. In addition, four gene transfer agent-like genes were found in the vB_PmaS-R3 genome. A putative L-alanoyl-D-glutamate peptidase was predicted as the endolysin. A MazG gene was found in the vB_PmaS-R3 genome, which indicates genomic adaption to the nutrient-limited marine environment.

No MeSH data available.