Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella)
Abstract Background A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09159-x |
| _version_ | 1827985137779867648 |
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| author | Huiqin Niu Yifan Pang Lingli Xie Qiaozhen Yu Yubang Shen Jiale Li Xiaoyan Xu |
| author_facet | Huiqin Niu Yifan Pang Lingli Xie Qiaozhen Yu Yubang Shen Jiale Li Xiaoyan Xu |
| author_sort | Huiqin Niu |
| collection | DOAJ |
| description | Abstract Background A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. Results The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. Conclusions This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost. |
| first_indexed | 2024-04-09T23:09:12Z |
| format | Article |
| id | doaj.art-c081928b446c42e3883bfc5366f41583 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:12Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c081928b446c42e3883bfc5366f415832023-03-22T10:30:55ZengBMCBMC Genomics1471-21642023-02-0124111410.1186/s12864-023-09159-xClustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella)Huiqin Niu0Yifan Pang1Lingli Xie2Qiaozhen Yu3Yubang Shen4Jiale Li5Xiaoyan Xu6Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityKey Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean UniversityAbstract Background A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. Results The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. Conclusions This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.https://doi.org/10.1186/s12864-023-09159-xmicroRNAmiRNA clustersGrass carpEvolutionPurifying selection |
| spellingShingle | Huiqin Niu Yifan Pang Lingli Xie Qiaozhen Yu Yubang Shen Jiale Li Xiaoyan Xu Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) BMC Genomics microRNA miRNA clusters Grass carp Evolution Purifying selection |
| title | Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) |
| title_full | Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) |
| title_fullStr | Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) |
| title_full_unstemmed | Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) |
| title_short | Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella) |
| title_sort | clustering pattern and evolution characteristic of micrornas in grass carp ctenopharyngodon idella |
| topic | microRNA miRNA clusters Grass carp Evolution Purifying selection |
| url | https://doi.org/10.1186/s12864-023-09159-x |
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