title: Global gene expression patterns of grass carp following compensatory growth.
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.
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. helibowudi@ihb.ac.cn.
authors.forename: Libo
authors.initials: L
authors.lastname: He
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. callmepyy@126.com.|University of Chinese Academy of Sciences, Beijing, 100049, China. callmepyy@126.com.
authors.forename: Yongyan
authors.initials: Y
authors.lastname: Pei
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. jyxboy@163.com.|University of Chinese Academy of Sciences, Beijing, 100049, China. jyxboy@163.com.
authors.forename: Yao
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. liyongming8080@sohu.com.
authors.forename: Yongming
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. liaolj@ihb.ac.cn.
authors.forename: Lanjie
authors.initials: L
authors.lastname: Liao
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. zyzhu@ihb.ac.cn.
authors.forename: Zuoyan
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. wangyp@ihb.ac.cn.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D001835:Body Weight; D002347:Carps / Q000235:genetics* / Q000254:growth & development*; D019295:Computational Biology; D005215:Fasting; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D015203:Reproducibility of Results; D059467:Transcriptome