Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus
As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus–host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting <i>Bacillus tequilensis</i>...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-09-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/9/1919 |
| _version_ | 1797576376918736896 |
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| author | Yuan Chen Tianyou Zhang Qiliang Lai Menghui Zhang Meishun Yu Runying Zeng Min Jin |
| author_facet | Yuan Chen Tianyou Zhang Qiliang Lai Menghui Zhang Meishun Yu Runying Zeng Min Jin |
| author_sort | Yuan Chen |
| collection | DOAJ |
| description | As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus–host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting <i>Bacillus tequilensis</i>, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0–33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under <i>Caudoviricetes</i>. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus–host interactions, as well as expanding our knowledge on phage taxonomy. |
| first_indexed | 2024-03-10T21:51:18Z |
| format | Article |
| id | doaj.art-36ea4834121b41828eeecaf7edfbfb3e |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T21:51:18Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-36ea4834121b41828eeecaf7edfbfb3e2023-11-19T13:23:34ZengMDPI AGViruses1999-49152023-09-01159191910.3390/v15091919Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel GenusYuan Chen0Tianyou Zhang1Qiliang Lai2Menghui Zhang3Meishun Yu4Runying Zeng5Min Jin6State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaFujian Provincial Center for Disease Control and Prevention, Fuzhou 350000, ChinaState Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaState Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaState Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaState Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaState Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, ChinaAs the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus–host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting <i>Bacillus tequilensis</i>, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0–33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under <i>Caudoviricetes</i>. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus–host interactions, as well as expanding our knowledge on phage taxonomy.https://www.mdpi.com/1999-4915/15/9/1919<i>Bacillus</i> phage<i>Bacillus tequilensis</i>myophagesdeep seanovel genus |
| spellingShingle | Yuan Chen Tianyou Zhang Qiliang Lai Menghui Zhang Meishun Yu Runying Zeng Min Jin Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus Viruses <i>Bacillus</i> phage <i>Bacillus tequilensis</i> myophages deep sea novel genus |
| title | Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus |
| title_full | Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus |
| title_fullStr | Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus |
| title_full_unstemmed | Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus |
| title_short | Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus |
| title_sort | characterization and comparative genomic analysis of a deep sea i bacillus i phage reveal a novel genus |
| topic | <i>Bacillus</i> phage <i>Bacillus tequilensis</i> myophages deep sea novel genus |
| url | https://www.mdpi.com/1999-4915/15/9/1919 |
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