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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.

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Venn diagram of DEGs between different comparisons. Overlapping regions represent DEGs in both comparisons. The size of the circle was made proportional to the number it represents. (A) Venn diagram of DEGs between E-1-M/C-1-M and E-1-L/C-1-L. (B) Venn diagram of DEGs between E-2-M/C-2-M and E-2-L/C-2-L. (C) Venn diagram of DEGs between E-2-M/E-1-M and E-2-L/E-1-L.
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Fig2: Venn diagram of DEGs between different comparisons. Overlapping regions represent DEGs in both comparisons. The size of the circle was made proportional to the number it represents. (A) Venn diagram of DEGs between E-1-M/C-1-M and E-1-L/C-1-L. (B) Venn diagram of DEGs between E-2-M/C-2-M and E-2-L/C-2-L. (C) Venn diagram of DEGs between E-2-M/E-1-M and E-2-L/E-1-L.

Mentions: From integration of the replicates, the 24 libraries were condensed into 8 sample groups named C-1-M, C-l-L, E-1-M, E-1-L, C-2-M, C-2-L, E-2-M, and E-2-L. To identify DEGs, samples were subjected to a series of paired-comparisons. Muscle and liver samples from the experimental group that experienced fasting conditions were compared with the appropriate control group (E-1-M/C-1-M and E-1-L/C-1-L). Muscle and liver samples from the experimental group following re-feeding were compared with the appropriate control group (E-2-M/C-2-M and E-2-L/C-2-L). In addition, muscle and liver samples from the experimental group following re-feeding were compared with experimental groups following fasting conditions (E-2-M/E-1-M and E-2-L/E-1-L). The number of DEGs identified from the different paired-comparisons is listed in Table 2. In fasting conditions, 4061 DEGs were detected in muscle (2124 up-regulated and 1937 down-regulated) and 1988 DEGs were identified in liver (761 up-regulated and 1227 down-regulated). Following re-feeding, 349 and 27 DEGs were discovered in muscle (281 up-regulated and 68 down-regulated) and liver (148 up-regulated and 99 down-regulated), respectively. Moreover, when fasting and re-feeding experimental groups were compared, 4903 DEGs were identified in muscle (2668 up-regulated and 2235 down-regulated) and 2444 DEGs were detected in liver (1512 up-regulated and 932 down-regulated). Detailed information of all DEGs is shown in Additional file 5. These DEGs were subjected to Venn diagram analysis (Figure 2), which identified 892 genes in both E-1-M/C-1-M and E-1-L/C-1-L (Figure 2A), 29 genes in both E-2-M/C-2-M and E-2-L/C-2-L (Figure 2B), and 1205 genes in both E-2-M/E-1-M andE-2-L/E-1-L (Figure 2C).Table 2


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)

Venn diagram of DEGs between different comparisons. Overlapping regions represent DEGs in both comparisons. The size of the circle was made proportional to the number it represents. (A) Venn diagram of DEGs between E-1-M/C-1-M and E-1-L/C-1-L. (B) Venn diagram of DEGs between E-2-M/C-2-M and E-2-L/C-2-L. (C) Venn diagram of DEGs between E-2-M/E-1-M and E-2-L/E-1-L.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374334&req=5

Fig2: Venn diagram of DEGs between different comparisons. Overlapping regions represent DEGs in both comparisons. The size of the circle was made proportional to the number it represents. (A) Venn diagram of DEGs between E-1-M/C-1-M and E-1-L/C-1-L. (B) Venn diagram of DEGs between E-2-M/C-2-M and E-2-L/C-2-L. (C) Venn diagram of DEGs between E-2-M/E-1-M and E-2-L/E-1-L.
Mentions: From integration of the replicates, the 24 libraries were condensed into 8 sample groups named C-1-M, C-l-L, E-1-M, E-1-L, C-2-M, C-2-L, E-2-M, and E-2-L. To identify DEGs, samples were subjected to a series of paired-comparisons. Muscle and liver samples from the experimental group that experienced fasting conditions were compared with the appropriate control group (E-1-M/C-1-M and E-1-L/C-1-L). Muscle and liver samples from the experimental group following re-feeding were compared with the appropriate control group (E-2-M/C-2-M and E-2-L/C-2-L). In addition, muscle and liver samples from the experimental group following re-feeding were compared with experimental groups following fasting conditions (E-2-M/E-1-M and E-2-L/E-1-L). The number of DEGs identified from the different paired-comparisons is listed in Table 2. In fasting conditions, 4061 DEGs were detected in muscle (2124 up-regulated and 1937 down-regulated) and 1988 DEGs were identified in liver (761 up-regulated and 1227 down-regulated). Following re-feeding, 349 and 27 DEGs were discovered in muscle (281 up-regulated and 68 down-regulated) and liver (148 up-regulated and 99 down-regulated), respectively. Moreover, when fasting and re-feeding experimental groups were compared, 4903 DEGs were identified in muscle (2668 up-regulated and 2235 down-regulated) and 2444 DEGs were detected in liver (1512 up-regulated and 932 down-regulated). Detailed information of all DEGs is shown in Additional file 5. These DEGs were subjected to Venn diagram analysis (Figure 2), which identified 892 genes in both E-1-M/C-1-M and E-1-L/C-1-L (Figure 2A), 29 genes in both E-2-M/C-2-M and E-2-L/C-2-L (Figure 2B), and 1205 genes in both E-2-M/E-1-M andE-2-L/E-1-L (Figure 2C).Table 2

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