Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae
Pseudomonas is a ubiquitous and ambiguous opportunistic pathogen, and plays an important ecological role in the ocean. Here, a new species, Pseudomonas phage vB_PaeM_M1, is described, which was isolated from the surface coastal waters of Qingdao, China. vB_PaeM_M1 contains a linear, double-stranded...
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.1076885/full |
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| author | Linyi Ren Yundan Liu Yantao Liang Baohong Liu Andrew McMinn Andrew McMinn Kaiyang Zheng Ziyue Wang Hongmin Wang Hongbing Shao Hongbing Shao Yeong Yik Sung Yeong Yik Sung Wen Jye Mok Wen Jye Mok Li Lian Wong Li Lian Wong Min Wang Min Wang Min Wang Min Wang |
| author_facet | Linyi Ren Yundan Liu Yantao Liang Baohong Liu Andrew McMinn Andrew McMinn Kaiyang Zheng Ziyue Wang Hongmin Wang Hongbing Shao Hongbing Shao Yeong Yik Sung Yeong Yik Sung Wen Jye Mok Wen Jye Mok Li Lian Wong Li Lian Wong Min Wang Min Wang Min Wang Min Wang |
| author_sort | Linyi Ren |
| collection | DOAJ |
| description | Pseudomonas is a ubiquitous and ambiguous opportunistic pathogen, and plays an important ecological role in the ocean. Here, a new species, Pseudomonas phage vB_PaeM_M1, is described, which was isolated from the surface coastal waters of Qingdao, China. vB_PaeM_M1 contains a linear, double-stranded 89,387-bp genome with a GC content of 41.04% and encoding 184 putative open reading frames (ORFs). There were 50 conservative domains were predicted with BLASTp, including two auxiliary metabolic genes (Phosphate-inducible gene phoH and signal peptide peptidase A, sppA). Phylogenetic analysis of whole genome amino acid sequence and comparative genomic analysis showed that vB_PaeM_M1 has a distant evolutionary relationship with previously isolated viruses and can be grouped into a family-level novel viral cluster (VC_61) with eleven uncultured, assembled viral genomes, named as Psaeviridae. Psaeviridae contains two ORFs (ORFs 117 and 127), which were not detected in the genomes of other viral families, confirming the proposal for a new family. Combined with its ability to infect Pseudomonas and its representation of an unstudied viral family, vB_PaeM_M1 may be an important and novel model system for the study of interactions between viruses and host cells in marine ecosystems. |
| format | Article |
| id | doaj-art-2d942938af7945d48ddff772afafaeed |
| institution | OA Journals |
| issn | 2296-7745 |
| language | English |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj-art-2d942938af7945d48ddff772afafaeed2025-08-20T02:24:55ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452022-12-01910.3389/fmars.2022.10768851076885Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, PsaeviridaeLinyi Ren0Yundan Liu1Yantao Liang2Baohong Liu3Andrew McMinn4Andrew McMinn5Kaiyang Zheng6Ziyue Wang7Hongmin Wang8Hongbing Shao9Hongbing Shao10Yeong Yik Sung11Yeong Yik Sung12Wen Jye Mok13Wen Jye Mok14Li Lian Wong15Li Lian Wong16Min Wang17Min Wang18Min Wang19Min Wang20College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaDepartment of Hospital Infection Management, Qilu Hospital, Shandong University, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaUMT-OUC Joint Centre for Marine Studies, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaInstitute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, AustraliaInstitute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, AustraliaInstitute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, MalaysiaInstitute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, AustraliaInstitute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, MalaysiaInstitute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, AustraliaInstitute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, MalaysiaCollege of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, ChinaInstitute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, AustraliaThe Affiliated Hospital of Qingdao University, Qingdao, ChinaHaide College, Ocean University of China, Qingdao, ChinaPseudomonas is a ubiquitous and ambiguous opportunistic pathogen, and plays an important ecological role in the ocean. Here, a new species, Pseudomonas phage vB_PaeM_M1, is described, which was isolated from the surface coastal waters of Qingdao, China. vB_PaeM_M1 contains a linear, double-stranded 89,387-bp genome with a GC content of 41.04% and encoding 184 putative open reading frames (ORFs). There were 50 conservative domains were predicted with BLASTp, including two auxiliary metabolic genes (Phosphate-inducible gene phoH and signal peptide peptidase A, sppA). Phylogenetic analysis of whole genome amino acid sequence and comparative genomic analysis showed that vB_PaeM_M1 has a distant evolutionary relationship with previously isolated viruses and can be grouped into a family-level novel viral cluster (VC_61) with eleven uncultured, assembled viral genomes, named as Psaeviridae. Psaeviridae contains two ORFs (ORFs 117 and 127), which were not detected in the genomes of other viral families, confirming the proposal for a new family. Combined with its ability to infect Pseudomonas and its representation of an unstudied viral family, vB_PaeM_M1 may be an important and novel model system for the study of interactions between viruses and host cells in marine ecosystems.https://www.frontiersin.org/articles/10.3389/fmars.2022.1076885/fullbacteriophagePseudomonasgenomic and comparative genomic analysisphylogenetic analysisPsaeviridae |
| spellingShingle | Linyi Ren Yundan Liu Yantao Liang Baohong Liu Andrew McMinn Andrew McMinn Kaiyang Zheng Ziyue Wang Hongmin Wang Hongbing Shao Hongbing Shao Yeong Yik Sung Yeong Yik Sung Wen Jye Mok Wen Jye Mok Li Lian Wong Li Lian Wong Min Wang Min Wang Min Wang Min Wang Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae Frontiers in Marine Science bacteriophage Pseudomonas genomic and comparative genomic analysis phylogenetic analysis Psaeviridae |
| title | Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae |
| title_full | Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae |
| title_fullStr | Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae |
| title_full_unstemmed | Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae |
| title_short | Characterization and genomic Analysis of a novel Pseudomonas phage vB_PaeM_M1, representing a new viral family, Psaeviridae |
| title_sort | characterization and genomic analysis of a novel pseudomonas phage vb paem m1 representing a new viral family psaeviridae |
| topic | bacteriophage Pseudomonas genomic and comparative genomic analysis phylogenetic analysis Psaeviridae |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.1076885/full |
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