Sipunculus nudus genome provides insights into evolution of spiralian phyla and development
IntroductionSipunculus nudus is the most known species in the genus Sipunculus, distributed in tropical and subtropical coastal waters.MethodsPacBio sequencing and Illumina sequencing were combined for whole-genome sequencing of S. nudus. LC-MS/MS analysis was performed for the metabolomics of S. nu...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.1043311/full |
| _version_ | 1797955319000727552 |
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| author | Yi Qi Yi Qi Liang Chen Binhua Wu Xiaoning Tang Xiao Zhu Ru Li Kefeng Wu Kefeng Wu Hui Luo Hui Luo |
| author_facet | Yi Qi Yi Qi Liang Chen Binhua Wu Xiaoning Tang Xiao Zhu Ru Li Kefeng Wu Kefeng Wu Hui Luo Hui Luo |
| author_sort | Yi Qi |
| collection | DOAJ |
| description | IntroductionSipunculus nudus is the most known species in the genus Sipunculus, distributed in tropical and subtropical coastal waters.MethodsPacBio sequencing and Illumina sequencing were combined for whole-genome sequencing of S. nudus. LC-MS/MS analysis was performed for the metabolomics of S. nudus.ResultsHerein, we report a 1.75 Gb complete genome assembly with a contig N50 size of 450 kb of the S. nudus based on a strategy combining third-generation long-read sequencing and Illumina sequencing. A total of 80391 protein-coding genes are annotated in this genome. Furthermore, gene family evolution analysis shows that S. nudus belonged to Mollusca or was close to Mollusca, but distinct with Annelida. Transcriptome analysis indicates the involvement of complex developmental events in larve. KEGG pathway analysis of differentially expressed genes showed that these DEGs were mainly enriched in the pathway of amino acid metabolism, lipid metabolism and transport and catabolism. LC-MS/MS analysis shows that S. nudus was rich in a variety of nutritional and functional components, such as carnitine, free amino acids, unsaturated fatty acids, inosine and methionine sulfoxide. Combined transcriptome with LC-MS/MS analysis, the results showed that gene expression and metabolic level involved in the inosine, arginine and proline biosynthesis of S. nudus during different growth stages were significantly changed.DiscussionOur genome assembly provides an important genome resource and new insight into the relationships of Sipuncula to other spiralian phyla. Meanwhile, transcriptome and LC-MS/MS analysis reveal the systematic gene expression profiles and metabolite components of S. nudus during different growth stages, which provide new insight into the exploration and development of bioactive molecules of S. nudus. |
| first_indexed | 2024-04-10T23:31:12Z |
| format | Article |
| id | doaj.art-e93f5b89144e44778b64c0299bb8b68d |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-10T23:31:12Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-e93f5b89144e44778b64c0299bb8b68d2023-01-12T06:44:36ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452023-01-01910.3389/fmars.2022.10433111043311Sipunculus nudus genome provides insights into evolution of spiralian phyla and developmentYi Qi0Yi Qi1Liang Chen2Binhua Wu3Xiaoning Tang4Xiao Zhu5Ru Li6Kefeng Wu7Kefeng Wu8Hui Luo9Hui Luo10Institute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaPharmacy Department, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, ChinaInstitute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaInstitute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaAffiliated Hospital of Guangdong Medical University Pharmacy Department, Zhanjiang, Guangdong, ChinaInstitute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, Guangdong, ChinaInstitute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaThe Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, Guangdong, ChinaInstitute of Marine Medicine, Guangdong Medical University, Zhanjiang, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, Guangdong, ChinaIntroductionSipunculus nudus is the most known species in the genus Sipunculus, distributed in tropical and subtropical coastal waters.MethodsPacBio sequencing and Illumina sequencing were combined for whole-genome sequencing of S. nudus. LC-MS/MS analysis was performed for the metabolomics of S. nudus.ResultsHerein, we report a 1.75 Gb complete genome assembly with a contig N50 size of 450 kb of the S. nudus based on a strategy combining third-generation long-read sequencing and Illumina sequencing. A total of 80391 protein-coding genes are annotated in this genome. Furthermore, gene family evolution analysis shows that S. nudus belonged to Mollusca or was close to Mollusca, but distinct with Annelida. Transcriptome analysis indicates the involvement of complex developmental events in larve. KEGG pathway analysis of differentially expressed genes showed that these DEGs were mainly enriched in the pathway of amino acid metabolism, lipid metabolism and transport and catabolism. LC-MS/MS analysis shows that S. nudus was rich in a variety of nutritional and functional components, such as carnitine, free amino acids, unsaturated fatty acids, inosine and methionine sulfoxide. Combined transcriptome with LC-MS/MS analysis, the results showed that gene expression and metabolic level involved in the inosine, arginine and proline biosynthesis of S. nudus during different growth stages were significantly changed.DiscussionOur genome assembly provides an important genome resource and new insight into the relationships of Sipuncula to other spiralian phyla. Meanwhile, transcriptome and LC-MS/MS analysis reveal the systematic gene expression profiles and metabolite components of S. nudus during different growth stages, which provide new insight into the exploration and development of bioactive molecules of S. nudus.https://www.frontiersin.org/articles/10.3389/fmars.2022.1043311/fullsipunculus nudusgenometranscriptomeevolutionmetabolite |
| spellingShingle | Yi Qi Yi Qi Liang Chen Binhua Wu Xiaoning Tang Xiao Zhu Ru Li Kefeng Wu Kefeng Wu Hui Luo Hui Luo Sipunculus nudus genome provides insights into evolution of spiralian phyla and development Frontiers in Marine Science sipunculus nudus genome transcriptome evolution metabolite |
| title | Sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| title_full | Sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| title_fullStr | Sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| title_full_unstemmed | Sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| title_short | Sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| title_sort | sipunculus nudus genome provides insights into evolution of spiralian phyla and development |
| topic | sipunculus nudus genome transcriptome evolution metabolite |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.1043311/full |
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