Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates
MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression at the post-transcriptional level. Characterized by their dynamic expression patterns, miRNAs play a crucial role in regulating a multitude of biological processes, including metabolism and autophagy. For fishermen, enha...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | Aquaculture Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235251342400615X |
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| author | Yuchen Wang Zhidong Zhang Suhua Chen Yangping Wu Qiujie Li Yi Cao Yu Zhang Aihua Chen |
| author_facet | Yuchen Wang Zhidong Zhang Suhua Chen Yangping Wu Qiujie Li Yi Cao Yu Zhang Aihua Chen |
| author_sort | Yuchen Wang |
| collection | DOAJ |
| description | MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression at the post-transcriptional level. Characterized by their dynamic expression patterns, miRNAs play a crucial role in regulating a multitude of biological processes, including metabolism and autophagy. For fishermen, enhancing the growth performance of the Asian hard clam, Meretrix meretrix, is vital for increasing yields and their income. To elucidating the regulatory mechanisms underlying clam growth, a comparative analysis of the miRNA and mRNA transcriptomes was undertaken for M. meretrix specimens exhibiting disparate growth rates. The results showed that a total of 32 differentially expressed miRNAs (DEMs) and 1049 differentially expressed mRNAs (DEGs) were identified. Furthermore, an integrated miRNA-mRNA expression analysis enabled the identification of 459 differentially predicted target genes (DETGs) associated with the DEMs. A significant enrichment in multiple functional categories related to metabolism and autophagy was observed among the DETGs. We constructed an intricate regulatory network that encompasses the metabolic and autophagy pathways influenced by 11 pivotal DEMs and 15 DETGs, which differ across the growth rates of M. meretrix. The results indicate that variations in growth rates elicit complex responses in both miRNA and mRNA expression, profoundly influencing the metabolic and autophagy processes within M. meretrix. |
| format | Article |
| id | doaj-art-6371b4ae762e4072be81be1e65f1f315 |
| institution | Kabale University |
| issn | 2352-5134 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj-art-6371b4ae762e4072be81be1e65f1f3152025-02-06T05:12:03ZengElsevierAquaculture Reports2352-51342025-03-0140102527Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth ratesYuchen Wang0Zhidong Zhang1Suhua Chen2Yangping Wu3Qiujie Li4Yi Cao5Yu Zhang6Aihua Chen7Marine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, ChinaMarine Economic Shellfish Research and Development Center of Jiangsu Province, Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; Corresponding author.MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression at the post-transcriptional level. Characterized by their dynamic expression patterns, miRNAs play a crucial role in regulating a multitude of biological processes, including metabolism and autophagy. For fishermen, enhancing the growth performance of the Asian hard clam, Meretrix meretrix, is vital for increasing yields and their income. To elucidating the regulatory mechanisms underlying clam growth, a comparative analysis of the miRNA and mRNA transcriptomes was undertaken for M. meretrix specimens exhibiting disparate growth rates. The results showed that a total of 32 differentially expressed miRNAs (DEMs) and 1049 differentially expressed mRNAs (DEGs) were identified. Furthermore, an integrated miRNA-mRNA expression analysis enabled the identification of 459 differentially predicted target genes (DETGs) associated with the DEMs. A significant enrichment in multiple functional categories related to metabolism and autophagy was observed among the DETGs. We constructed an intricate regulatory network that encompasses the metabolic and autophagy pathways influenced by 11 pivotal DEMs and 15 DETGs, which differ across the growth rates of M. meretrix. The results indicate that variations in growth rates elicit complex responses in both miRNA and mRNA expression, profoundly influencing the metabolic and autophagy processes within M. meretrix.http://www.sciencedirect.com/science/article/pii/S235251342400615XMeretrix meretrixmiRNA-mRNAGrowthMetabolismAutophagy |
| spellingShingle | Yuchen Wang Zhidong Zhang Suhua Chen Yangping Wu Qiujie Li Yi Cao Yu Zhang Aihua Chen Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates Aquaculture Reports Meretrix meretrix miRNA-mRNA Growth Metabolism Autophagy |
| title | Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates |
| title_full | Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates |
| title_fullStr | Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates |
| title_full_unstemmed | Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates |
| title_short | Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates |
| title_sort | comprehensive assessment of a mirna mrna regulatory network in meretrix meretrix implications for metabolism and autophagy across divergent growth rates |
| topic | Meretrix meretrix miRNA-mRNA Growth Metabolism Autophagy |
| url | http://www.sciencedirect.com/science/article/pii/S235251342400615X |
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