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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
Gene ontology of the top 30 enriched terms in different comparisons. Annotated genes were placed in three main categories, namely biological process, molecular function, and cellular component. The number of genes in each comparison is shown. A, E-1-M/C-1-M; B, E-1-L/C-1-L; C, E-2-M/C-2-M; D, E-2-L/C-2-L; E, E-2-M/E-1-M; F, E-2-L/E-1-L.
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Fig3: Gene ontology of the top 30 enriched terms in different comparisons. Annotated genes were placed in three main categories, namely biological process, molecular function, and cellular component. The number of genes in each comparison is shown. A, E-1-M/C-1-M; B, E-1-L/C-1-L; C, E-2-M/C-2-M; D, E-2-L/C-2-L; E, E-2-M/E-1-M; F, E-2-L/E-1-L.

Mentions: GO enrichment analysis was performed to investigate the possible roles of DEGs. For all six paired-comparisons, annotated genes were categorized into three main categories, namely biological process, molecular function, and cellular component (FigureĀ 3, top 30 most enriched terms). The biological process category included high representation for genes involved in single-organism metabolic processes, organonitrogen compound metabolism, small molecule metabolism, oxidation-reduction, general metabolic and organic acid metabolic processes. Catalytic activity, oxidoreductase activity, cofactor binding, coenzyme binding, and other binding terms were significant enriched in the molecular function category. In the cellular component category, intracellular, myosin complex, extracellular matrix, actin cytoskeleton, and non-membrane-bound organelle terms were abundant. In the comparison of E-2-L/C-2-L, no cellular component term was enriched, and the number of terms for biological process and molecular function was also low. Detailed information of enriched terms is listed in Additional file 6.Figure 3


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)

Gene ontology of the top 30 enriched terms in different comparisons. Annotated genes were placed in three main categories, namely biological process, molecular function, and cellular component. The number of genes in each comparison is shown. A, E-1-M/C-1-M; B, E-1-L/C-1-L; C, E-2-M/C-2-M; D, E-2-L/C-2-L; E, E-2-M/E-1-M; F, 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

Fig3: Gene ontology of the top 30 enriched terms in different comparisons. Annotated genes were placed in three main categories, namely biological process, molecular function, and cellular component. The number of genes in each comparison is shown. A, E-1-M/C-1-M; B, E-1-L/C-1-L; C, E-2-M/C-2-M; D, E-2-L/C-2-L; E, E-2-M/E-1-M; F, E-2-L/E-1-L.
Mentions: GO enrichment analysis was performed to investigate the possible roles of DEGs. For all six paired-comparisons, annotated genes were categorized into three main categories, namely biological process, molecular function, and cellular component (FigureĀ 3, top 30 most enriched terms). The biological process category included high representation for genes involved in single-organism metabolic processes, organonitrogen compound metabolism, small molecule metabolism, oxidation-reduction, general metabolic and organic acid metabolic processes. Catalytic activity, oxidoreductase activity, cofactor binding, coenzyme binding, and other binding terms were significant enriched in the molecular function category. In the cellular component category, intracellular, myosin complex, extracellular matrix, actin cytoskeleton, and non-membrane-bound organelle terms were abundant. In the comparison of E-2-L/C-2-L, no cellular component term was enriched, and the number of terms for biological process and molecular function was also low. Detailed information of enriched terms is listed in Additional file 6.Figure 3

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