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Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia.

Sun S, Xuan F, Fu H, Zhu J, Ge X, Gu Z - BMC Genomics (2015)

Bottom Line: Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China.However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown.Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories "response to stimulus", "transferase activity" and "oxidoreductase activity", and the signaling pathways "oxidative phosphorylation", "glycolysis/gluconeogenesis" and "MAPK signaling".

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, People's Republic of China. sunshengming621416@163.com.

ABSTRACT

Background: Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, and the hepatopancreas, muscle and gill tissues play important roles in adaptive processes. However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown. Adaptation to hypoxia is a complex process, to help us understand stress-sensing mechanism and ultimately permit selection for hypoxia- tolerant prawns, we performed transcriptomic analysis of juvenile M. nipponense hepatopancreas, gill and muscle tissues by RNA-Seq.

Results: Approximately 46,472,741; 52,773,612 and 58,195,908 raw sequence reads were generated from hepatopancreas, muscle and gill tissues, respectively. A total of 62,722 unigenes were generated, of the assembled unigenes, we identified 8,892 genes that were significantly up-regulated, while 5,760 genes were significantly down-regulated in response to chronic hypoxia. Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories "response to stimulus", "transferase activity" and "oxidoreductase activity", and the signaling pathways "oxidative phosphorylation", "glycolysis/gluconeogenesis" and "MAPK signaling". The expression patterns of 18 DEGs involved in hypoxic regulation of M. nipponense were validated by quantitative real-time reverse-transcriptase polymerase chain reactions (qRT-PCR; average correlation coefficient = 0.94). In addition, the hepatopancreas and gills exhibited histological differences between hypoxia and normoxia groups. These structural alterations could affect the vital physiological functions of prawns in response to chronic hypoxia, which could adversely affect growth and survival of M. nipponense.

Conclusions: Gene expression changes in tissues from the oriental river prawn provide a preliminary basis to better understand the molecular responses of M. nipponense to chronic hypoxia. The differentially expressed genes (DEGs) identified in M. nipponense under hypoxia stress may be important for future genetic improvement of cultivated prawns or other crustaceans through transgenic approaches aimed at increasing hypoxia tolerance.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. The x-axis shows genes in the three tissues validated in this study; the y-axis shows Log2Ratio of expression in Macrobrachium nipponense in response to hypoxia versus normoxia conditions
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Fig5: Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. The x-axis shows genes in the three tissues validated in this study; the y-axis shows Log2Ratio of expression in Macrobrachium nipponense in response to hypoxia versus normoxia conditions

Mentions: To validate the RNA-Seq results, 18 genes showing a high level of significance or known to play an important role in stress response functions were selected for qRT-PCR analysis with β-actin acting as the reference gene (Table 4). No significant differences were shown between qRT-PCR and the Illumina data (Pearson’s correlation coefficient r = 0.94) (Fig. 5). In addition, a number of detoxification-related genes, such as GST and HSP, were also found to be specifically expressed in different tissues of M. nipponense in response to chronic hypoxia. These genes have been shown to be hypoxia-responsive in other studies [12, 21, 22], and they are involved in antioxidant abilities, immune responses, glycolysis and apoptosis, which are important functions for maintaining and re-establishing homeostasis in response to pathological changes. We also found that many genes related to mitochondrial respiration were significantly down-regulated under hypoxia stress according to qRT-PCR, such as cytochrome c oxidase subunit I (CCO I), cytochrome oxidase I (COX I), NADH dehydrogenase subunit 1 (Complex I) and carbonic anhydrase I (CA I), which reveals that normal mitochondrial function was disrupted by oxidative stress. As mitochondrial respiration is affected in many pathologic conditions such as hypoxia and intoxications, the impaired electron transport chain could emit additional p53-inducing signals and thereby contribute to tissue damage [64]. We identified glycolysis related-genes from the DEG list for the muscle, and proPO, CTL, β-1,3-glucan binding protein (LGBP) and α2 M genes from the DEG list for the gill. Obviously, several genes could potentially be used as molecular indicators of hypoxia in M. nipponense at specific time points. However, the changes in the expression of these significant genes were too dynamic to serve as biomarkers of hypoxia stress in M. nipponense.


Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia.

Sun S, Xuan F, Fu H, Zhu J, Ge X, Gu Z - BMC Genomics (2015)

Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. The x-axis shows genes in the three tissues validated in this study; the y-axis shows Log2Ratio of expression in Macrobrachium nipponense in response to hypoxia versus normoxia conditions
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4490754&req=5

Fig5: Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. The x-axis shows genes in the three tissues validated in this study; the y-axis shows Log2Ratio of expression in Macrobrachium nipponense in response to hypoxia versus normoxia conditions
Mentions: To validate the RNA-Seq results, 18 genes showing a high level of significance or known to play an important role in stress response functions were selected for qRT-PCR analysis with β-actin acting as the reference gene (Table 4). No significant differences were shown between qRT-PCR and the Illumina data (Pearson’s correlation coefficient r = 0.94) (Fig. 5). In addition, a number of detoxification-related genes, such as GST and HSP, were also found to be specifically expressed in different tissues of M. nipponense in response to chronic hypoxia. These genes have been shown to be hypoxia-responsive in other studies [12, 21, 22], and they are involved in antioxidant abilities, immune responses, glycolysis and apoptosis, which are important functions for maintaining and re-establishing homeostasis in response to pathological changes. We also found that many genes related to mitochondrial respiration were significantly down-regulated under hypoxia stress according to qRT-PCR, such as cytochrome c oxidase subunit I (CCO I), cytochrome oxidase I (COX I), NADH dehydrogenase subunit 1 (Complex I) and carbonic anhydrase I (CA I), which reveals that normal mitochondrial function was disrupted by oxidative stress. As mitochondrial respiration is affected in many pathologic conditions such as hypoxia and intoxications, the impaired electron transport chain could emit additional p53-inducing signals and thereby contribute to tissue damage [64]. We identified glycolysis related-genes from the DEG list for the muscle, and proPO, CTL, β-1,3-glucan binding protein (LGBP) and α2 M genes from the DEG list for the gill. Obviously, several genes could potentially be used as molecular indicators of hypoxia in M. nipponense at specific time points. However, the changes in the expression of these significant genes were too dynamic to serve as biomarkers of hypoxia stress in M. nipponense.

Bottom Line: Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China.However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown.Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories "response to stimulus", "transferase activity" and "oxidoreductase activity", and the signaling pathways "oxidative phosphorylation", "glycolysis/gluconeogenesis" and "MAPK signaling".

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, People's Republic of China. sunshengming621416@163.com.

ABSTRACT

Background: Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, and the hepatopancreas, muscle and gill tissues play important roles in adaptive processes. However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown. Adaptation to hypoxia is a complex process, to help us understand stress-sensing mechanism and ultimately permit selection for hypoxia- tolerant prawns, we performed transcriptomic analysis of juvenile M. nipponense hepatopancreas, gill and muscle tissues by RNA-Seq.

Results: Approximately 46,472,741; 52,773,612 and 58,195,908 raw sequence reads were generated from hepatopancreas, muscle and gill tissues, respectively. A total of 62,722 unigenes were generated, of the assembled unigenes, we identified 8,892 genes that were significantly up-regulated, while 5,760 genes were significantly down-regulated in response to chronic hypoxia. Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories "response to stimulus", "transferase activity" and "oxidoreductase activity", and the signaling pathways "oxidative phosphorylation", "glycolysis/gluconeogenesis" and "MAPK signaling". The expression patterns of 18 DEGs involved in hypoxic regulation of M. nipponense were validated by quantitative real-time reverse-transcriptase polymerase chain reactions (qRT-PCR; average correlation coefficient = 0.94). In addition, the hepatopancreas and gills exhibited histological differences between hypoxia and normoxia groups. These structural alterations could affect the vital physiological functions of prawns in response to chronic hypoxia, which could adversely affect growth and survival of M. nipponense.

Conclusions: Gene expression changes in tissues from the oriental river prawn provide a preliminary basis to better understand the molecular responses of M. nipponense to chronic hypoxia. The differentially expressed genes (DEGs) identified in M. nipponense under hypoxia stress may be important for future genetic improvement of cultivated prawns or other crustaceans through transgenic approaches aimed at increasing hypoxia tolerance.

No MeSH data available.


Related in: MedlinePlus