Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes
文献类型：期刊论文
| 作者 | Kong, Deming3,4; Gan, Zhibin3; Li, Xinzheng1,2,3,4 |
| 刊名 | GENE
 |
| 出版日期 | 2024-02-20 |
| 卷号 | 896页码:14 |
| 关键词 | Caridea Adaptive evolution Deep-sea Mitogenome Phylogeny |
| ISSN号 | 0378-1119 |
| DOI | 10.1016/j.gene.2023.148054 |
| 通讯作者 | Gan, Zhibin(ganzhibin@qdio.ac.cn) ; Li, Xinzheng(lixzh@qdio.ac.cn) |
| 英文摘要 | The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment. |
| WOS关键词 | COMPLETE MITOCHONDRIAL GENOME ; CRUSTACEA DECAPODA CARIDEA ; HIGH-ALTITUDE ADAPTATION ; TRANSFER-RNA GENES ; ADAPTIVE EVOLUTION ; LOBSTERS CRUSTACEA ; POSITIVE SELECTION ; SHRIMPS CRUSTACEA ; SEQUENCE ; ALVINOCARIDIDAE |
| 资助项目 | National Natural Science Foundation of China[31970491] ; National Natural Science Foundation of China[41876178] ; Biological Resources Programme, Chinese Academy of Sciences[KFJ-BRP-017-094] |
| WOS研究方向 | Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:001135481700001 |
| 出版者 | ELSEVIER |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/199647]  |
| 专题 | 中国科学院海洋研究所 |
| 通讯作者 | Gan, Zhibin; Li, Xinzheng |
| 作者单位 | 1.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Qingdao, Peoples R China 4.Univ Chinese Acad Sci, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Kong, Deming,Gan, Zhibin,Li, Xinzheng. Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes[J]. GENE,2024,896:14. |
| APA | Kong, Deming,Gan, Zhibin,&Li, Xinzheng.(2024).Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes.GENE,896,14. |
| MLA | Kong, Deming,et al."Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes".GENE 896(2024):14. |
入库方式： OAI收割
来源：海洋研究所
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