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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

Length distribution of assembled transcriptome unigenes from Macrobrachium nipponense. The x-axis indicates contig size and the y-axis indicates the number of unigenes of each size
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Fig1: Length distribution of assembled transcriptome unigenes from Macrobrachium nipponense. The x-axis indicates contig size and the y-axis indicates the number of unigenes of each size

Mentions: To provide comprehensive understanding of expression differences between M. nipponense cultured in normoxic and hypoxic conditions, we collected and deep sequenced RNA samples from hepatopancreas, muscle and gill tissues. A total of 308,348,065 paired-end reads were generated from six samples with 101-bp read length. The number of sequences in each sample ranged from 45.6 to 58.2 million (Table 1). After removal of ambiguous nucleotides, low-quality sequences (Phred quality scores <20), contaminated microbial sequences and ribosomal RNA sequences, a total of 265,294,865 cleaned reads (86 %) were harvested for further analysis. The cleaned sequences in each sample ranged from 31.5 to 52.7 million reads, thus confirming the stability and consistency of sampling, library preparation and sequencing methodologies. Using the Trinity assembly program, we generated a total of 62,722 unigenes, the average length was 960 bp, and the N50 length was 1,450 bp. (Table 2). The length distribution of unigenes is shown in Fig. 1. The cleaned reads of the six samples were pooled and assembled by the Trinity assembler to generate a reference transcriptome assoiated with published EST datas [29]. According to Gene Ontology (GO), an internationally standardized gene functional classification system, 11,104 non-redundant unigenes were classified into three major functional categories (biological process, cellular component and molecular function).Table 1


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)

Length distribution of assembled transcriptome unigenes from Macrobrachium nipponense. The x-axis indicates contig size and the y-axis indicates the number of unigenes of each size
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Length distribution of assembled transcriptome unigenes from Macrobrachium nipponense. The x-axis indicates contig size and the y-axis indicates the number of unigenes of each size
Mentions: To provide comprehensive understanding of expression differences between M. nipponense cultured in normoxic and hypoxic conditions, we collected and deep sequenced RNA samples from hepatopancreas, muscle and gill tissues. A total of 308,348,065 paired-end reads were generated from six samples with 101-bp read length. The number of sequences in each sample ranged from 45.6 to 58.2 million (Table 1). After removal of ambiguous nucleotides, low-quality sequences (Phred quality scores <20), contaminated microbial sequences and ribosomal RNA sequences, a total of 265,294,865 cleaned reads (86 %) were harvested for further analysis. The cleaned sequences in each sample ranged from 31.5 to 52.7 million reads, thus confirming the stability and consistency of sampling, library preparation and sequencing methodologies. Using the Trinity assembly program, we generated a total of 62,722 unigenes, the average length was 960 bp, and the N50 length was 1,450 bp. (Table 2). The length distribution of unigenes is shown in Fig. 1. The cleaned reads of the six samples were pooled and assembled by the Trinity assembler to generate a reference transcriptome assoiated with published EST datas [29]. According to Gene Ontology (GO), an internationally standardized gene functional classification system, 11,104 non-redundant unigenes were classified into three major functional categories (biological process, cellular component and molecular function).Table 1

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