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Global gene expression patterns of grass carp following compensatory growth.

He L, Pei Y, Jiang Y, Li Y, Liao L, Zhu Z, Wang Y - BMC Genomics (2015)

Bottom Line: Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome.Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver.The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. helibowudi@ihb.ac.cn.

ABSTRACT

Background: Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes.

Results: In the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR.

Conclusions: Global gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.

Show MeSH
Validation of DEGs by qPCR. Twelve DEGs were random selected for qPCR analysis and compared with the equivalent RNA-seq data. The data from qPCR were presented as mean ± standard deviation of three replicates. The data from RNA-seq were the read counts that normalized by DEseq from three replicates. A and B, Expression level of MIF and PRDX3 in comparison E-1-M/C-1-M (grey bars, C-1-M; black bars, E-1-M); C and D, APOEb and EF-1α in comparison E-1-L/C-1-L (grey bars, C-1-L; black bars, E-1-L); E and F, APOA-I-1 and PAIP2B in comparison E-2-M/C-2-M (grey bars, C-2-M; black bars, E-2-M); G and H, PSD2 and ALDOb in E-2-L/C-2-L (grey bars, C-2-L; black bars, E-2-L); I and J, ALDOa and CFD in E-2-M/E-1-M (grey bars, E-1-M; black bars, E-2-M); K and L, EFF1α1L2 and GAPDH in E-2-L/E-1-L (grey bars, E-1-L; black bars, E-2-L).
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Fig4: Validation of DEGs by qPCR. Twelve DEGs were random selected for qPCR analysis and compared with the equivalent RNA-seq data. The data from qPCR were presented as mean ± standard deviation of three replicates. The data from RNA-seq were the read counts that normalized by DEseq from three replicates. A and B, Expression level of MIF and PRDX3 in comparison E-1-M/C-1-M (grey bars, C-1-M; black bars, E-1-M); C and D, APOEb and EF-1α in comparison E-1-L/C-1-L (grey bars, C-1-L; black bars, E-1-L); E and F, APOA-I-1 and PAIP2B in comparison E-2-M/C-2-M (grey bars, C-2-M; black bars, E-2-M); G and H, PSD2 and ALDOb in E-2-L/C-2-L (grey bars, C-2-L; black bars, E-2-L); I and J, ALDOa and CFD in E-2-M/E-1-M (grey bars, E-1-M; black bars, E-2-M); K and L, EFF1α1L2 and GAPDH in E-2-L/E-1-L (grey bars, E-1-L; black bars, E-2-L).

Mentions: To confirm the RNA-seq data, twelve DEGs were random selected for qPCR analysis. The RNA samples that form an independent repeated study and were used for reverse transcription and qPCR analysis. For each of paired-comparison, two genes were random selected. The random selected DEGs were macrophage migration inhibitory factor (MIF),peroxiredoxin 3 (PRDX3), apolipoprotein Eb (APOEb), elongation factor 1-alpha (EF-1a), apolipoprotein A-I-1 (APOA-I-1), poly (A) binding protein interacting protein 2B (PAIP2B), pleckstrin and Sec7 domain containing 2 (PSD2), fructose-bisphosphate aldolase b (ALDOb), fructose-bisphosphate aldolase a (ALDOa), complement factor D (CFD), eukaryotic translation elongation factor 1 alpha 1-like 2 (EFF1a1L2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH). As shown in Figure 4, the expression patterns of all twelve DEGs that obtained by qPCR were similar to that in RNA-seq, although the relative expression level was not completely consistent. The results confirmed the reliability and accuracy of the RNA-seq data (Figure 4).Figure 4


Global gene expression patterns of grass carp following compensatory growth.

He L, Pei Y, Jiang Y, Li Y, Liao L, Zhu Z, Wang Y - BMC Genomics (2015)

Validation of DEGs by qPCR. Twelve DEGs were random selected for qPCR analysis and compared with the equivalent RNA-seq data. The data from qPCR were presented as mean ± standard deviation of three replicates. The data from RNA-seq were the read counts that normalized by DEseq from three replicates. A and B, Expression level of MIF and PRDX3 in comparison E-1-M/C-1-M (grey bars, C-1-M; black bars, E-1-M); C and D, APOEb and EF-1α in comparison E-1-L/C-1-L (grey bars, C-1-L; black bars, E-1-L); E and F, APOA-I-1 and PAIP2B in comparison E-2-M/C-2-M (grey bars, C-2-M; black bars, E-2-M); G and H, PSD2 and ALDOb in E-2-L/C-2-L (grey bars, C-2-L; black bars, E-2-L); I and J, ALDOa and CFD in E-2-M/E-1-M (grey bars, E-1-M; black bars, E-2-M); K and L, EFF1α1L2 and GAPDH in E-2-L/E-1-L (grey bars, E-1-L; black bars, E-2-L).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig4: Validation of DEGs by qPCR. Twelve DEGs were random selected for qPCR analysis and compared with the equivalent RNA-seq data. The data from qPCR were presented as mean ± standard deviation of three replicates. The data from RNA-seq were the read counts that normalized by DEseq from three replicates. A and B, Expression level of MIF and PRDX3 in comparison E-1-M/C-1-M (grey bars, C-1-M; black bars, E-1-M); C and D, APOEb and EF-1α in comparison E-1-L/C-1-L (grey bars, C-1-L; black bars, E-1-L); E and F, APOA-I-1 and PAIP2B in comparison E-2-M/C-2-M (grey bars, C-2-M; black bars, E-2-M); G and H, PSD2 and ALDOb in E-2-L/C-2-L (grey bars, C-2-L; black bars, E-2-L); I and J, ALDOa and CFD in E-2-M/E-1-M (grey bars, E-1-M; black bars, E-2-M); K and L, EFF1α1L2 and GAPDH in E-2-L/E-1-L (grey bars, E-1-L; black bars, E-2-L).
Mentions: To confirm the RNA-seq data, twelve DEGs were random selected for qPCR analysis. The RNA samples that form an independent repeated study and were used for reverse transcription and qPCR analysis. For each of paired-comparison, two genes were random selected. The random selected DEGs were macrophage migration inhibitory factor (MIF),peroxiredoxin 3 (PRDX3), apolipoprotein Eb (APOEb), elongation factor 1-alpha (EF-1a), apolipoprotein A-I-1 (APOA-I-1), poly (A) binding protein interacting protein 2B (PAIP2B), pleckstrin and Sec7 domain containing 2 (PSD2), fructose-bisphosphate aldolase b (ALDOb), fructose-bisphosphate aldolase a (ALDOa), complement factor D (CFD), eukaryotic translation elongation factor 1 alpha 1-like 2 (EFF1a1L2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH). As shown in Figure 4, the expression patterns of all twelve DEGs that obtained by qPCR were similar to that in RNA-seq, although the relative expression level was not completely consistent. The results confirmed the reliability and accuracy of the RNA-seq data (Figure 4).Figure 4

Bottom Line: Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome.Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver.The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. helibowudi@ihb.ac.cn.

ABSTRACT

Background: Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes.

Results: In the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR.

Conclusions: Global gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.

Show MeSH