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Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia
Published on: May 13, 2014
Transcriptomic WGCNA analyses reveal sectional regulatory mechanisms in giant freshwater prawn Macrobrachium
Yaoran Fan1, Lei Cao1, Yaorui Liang1
1Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
Abstract:
Hypoxia is a considerable challenge for the prawn culture, especially in high-density intensive aquaculture. The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species in Asia and South America. However, M. rosenbgergii larvae typically exhibit low resistance to hypoxic stress. To explore the molecular mechanism of hypoxia-reoxygenation on M. rosenbergii larvae, the transcriptomic WGCNA analysis was conducted to detect the dynamic regulatory mechanisms of M. rosenbergii larvae under 4, 8, 12, 24, 48, 72 h of hypoxia stress and 4, 12 h of reoxygenation stress. The results showed that a total of 3173 differentially expressed genes (DEGs) were identified in the gills (1812 up-regulated, 1361 down-regulated), 397 in the hepatopancreas (171 up-regulated, 226 down-regulated), and 768 in the muscle (374 up-regulated, 394 down-regulated). The gills were labeled as the primary functional organ by significantly abundant DEGs during hypoxia-reoxygenation. Additionally, 22 DEGs of 9 gene families were co-expressed during hypoxia-reoxygenation, including the cell protein (CP), cathelicidin associated protein (CAP), aminocyclopropane-1-carboxylate oxidase (ACO) families, etc. For the GO analysis during hypoxia-reoxygenation, the DEGs were mainly enriched in the cellular component and molecular function terms, including nucleolus, mitochondrion, and mRNA binding terms. Besides, the DEGs during hypoxia were significantly enriched in genetic and environmental information pathways involving the HIF-1 signaling pathway and ribosome. Additionally, the DEGs during reoxygenation were mainly associated with cellular processes, including lysosome, phagosome, and apoptosis. Furthermore, 30 candidate hypoxia-reoxygenation module-related DEGs were screened by WGCNA, involving SpAN, TIF-2, Titin, ATP binding cassette, L-ThrDH, G6DP, etc. Overall, these results may reveal the immunological regulatory mechanisms of M. rosenbergii larvae under hypoxia-reoxygenation stress and enrich practical reference materials underlying high-density intensive aquaculture.
