Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i>
<i>Macrobrachium rosenbergii</i> is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regul...
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MDPI AG
2023-03-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/3/460 |
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| author | Dong Liu Zhenzhen Hong Lang Gui Li Zhao Yude Wang Shengming Sun Mingyou Li |
| author_facet | Dong Liu Zhenzhen Hong Lang Gui Li Zhao Yude Wang Shengming Sun Mingyou Li |
| author_sort | Dong Liu |
| collection | DOAJ |
| description | <i>Macrobrachium rosenbergii</i> is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regulating life functions. In the present work, we applied PacBio RNA-seq to obtain and characterize the full-length transcriptomes of the brains and thoracic ganglia of female and male prawns, and we performed comparative transcriptome analysis of female and male prawns. A total of 159.1-Gb of subreads were obtained with an average length of 2175 bp and 93.2% completeness. A total of 84,627 high-quality unigenes were generated and annotated with functional databases. A total of 6367 transcript factors and 6287 LncRNAs were predicted. In total, 5287 and 6211 significantly differentially expressed genes (DEGs) were found in the brain and thoracic ganglion, respectively, and confirmed by qRT-PCR. Of the 435 genes associated with protein processing pathways in the endoplasmic reticula, 42 DEGs were detected, and 21/26 DEGs with upregulated expression in the male brain/thoracic ganglion. The DEGs in this pathway are regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our results provide novel theories and insights for studying the nervous system, sexual control, and growth dimorphism. |
| first_indexed | 2024-03-11T06:53:05Z |
| format | Article |
| id | doaj.art-ef5924a25ee64be6ac8cf585b6a4e453 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T06:53:05Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
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| series | Biomolecules |
| spelling | doaj.art-ef5924a25ee64be6ac8cf585b6a4e4532023-11-17T09:51:36ZengMDPI AGBiomolecules2218-273X2023-03-0113346010.3390/biom13030460Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i>Dong Liu0Zhenzhen Hong1Lang Gui2Li Zhao3Yude Wang4Shengming Sun5Mingyou Li6Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, ChinaState Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China<i>Macrobrachium rosenbergii</i> is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regulating life functions. In the present work, we applied PacBio RNA-seq to obtain and characterize the full-length transcriptomes of the brains and thoracic ganglia of female and male prawns, and we performed comparative transcriptome analysis of female and male prawns. A total of 159.1-Gb of subreads were obtained with an average length of 2175 bp and 93.2% completeness. A total of 84,627 high-quality unigenes were generated and annotated with functional databases. A total of 6367 transcript factors and 6287 LncRNAs were predicted. In total, 5287 and 6211 significantly differentially expressed genes (DEGs) were found in the brain and thoracic ganglion, respectively, and confirmed by qRT-PCR. Of the 435 genes associated with protein processing pathways in the endoplasmic reticula, 42 DEGs were detected, and 21/26 DEGs with upregulated expression in the male brain/thoracic ganglion. The DEGs in this pathway are regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our results provide novel theories and insights for studying the nervous system, sexual control, and growth dimorphism.https://www.mdpi.com/2218-273X/13/3/460prawnRNA-seqgenesignal pathwayLncRNA |
| spellingShingle | Dong Liu Zhenzhen Hong Lang Gui Li Zhao Yude Wang Shengming Sun Mingyou Li Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> Biomolecules prawn RNA-seq gene signal pathway LncRNA |
| title | Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> |
| title_full | Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> |
| title_fullStr | Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> |
| title_full_unstemmed | Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> |
| title_short | Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn <i>Macrobrachium rosenbergii</i> |
| title_sort | full length transcriptomes and sex based differentially expressed genes in the brain and ganglia of giant river prawn i macrobrachium rosenbergii i |
| topic | prawn RNA-seq gene signal pathway LncRNA |
| url | https://www.mdpi.com/2218-273X/13/3/460 |
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