The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus
Abstract Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can c...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-00565-3 |
| _version_ | 1818851431075020800 |
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| author | Yuki Hongo Kei Kimura Yoshihiro Takaki Yukari Yoshida Shuichiro Baba Genta Kobayashi Keizo Nagasaki Takeshi Hano Yuji Tomaru |
| author_facet | Yuki Hongo Kei Kimura Yoshihiro Takaki Yukari Yoshida Shuichiro Baba Genta Kobayashi Keizo Nagasaki Takeshi Hano Yuji Tomaru |
| author_sort | Yuki Hongo |
| collection | DOAJ |
| description | Abstract Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship. |
| first_indexed | 2024-12-19T07:04:55Z |
| format | Article |
| id | doaj.art-971dcd76a553480d9eb551b5a36b7a3d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T07:04:55Z |
| publishDate | 2021-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-971dcd76a553480d9eb551b5a36b7a3d2022-12-21T20:31:19ZengNature PortfolioScientific Reports2045-23222021-11-0111111310.1038/s41598-021-00565-3The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virusYuki Hongo0Kei Kimura1Yoshihiro Takaki2Yukari Yoshida3Shuichiro Baba4Genta Kobayashi5Keizo Nagasaki6Takeshi Hano7Yuji Tomaru8Fisheries Resources Institute, Japan Fisheries Research and Education AgencyFaculty of Agriculture, Saga UniversitySuper-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and TechnologySuper-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and TechnologyUnited Graduate School of Agricultural Sciences, Kagoshima UniversityFaculty of Agriculture, Saga UniversityFaculty of Science and Technology, Kochi UniversityFisheries Technology Institute, Japan Fisheries Research and Education AgencyFisheries Technology Institute, Japan Fisheries Research and Education AgencyAbstract Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship.https://doi.org/10.1038/s41598-021-00565-3 |
| spellingShingle | Yuki Hongo Kei Kimura Yoshihiro Takaki Yukari Yoshida Shuichiro Baba Genta Kobayashi Keizo Nagasaki Takeshi Hano Yuji Tomaru The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus Scientific Reports |
| title | The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| title_full | The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| title_fullStr | The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| title_full_unstemmed | The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| title_short | The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| title_sort | genome of the diatom chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus |
| url | https://doi.org/10.1038/s41598-021-00565-3 |
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