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De novo RNA sequencing for identification of growth-related genes in Silurus lanzhouensis muscle tissues

Abstract

To obtain transcriptomic insights into the growth regulation traits of Silurus lanzhouensis, this study employed de novo RNA sequencing to analyze the muscle transcriptome of the three heaviest (SLA) and three lightest (SLB) individuals from the same S. lanzhouensis family. Notably, the body weight, total length, and head length of the two groups were found to be significantly different (unpaired t test, P < 0.05). A total of 163,949 transcripts and 89,579 genes were identified, of which 843 differentially expressed genes (DEGs) were identified between the two groups (366 up-regulated and 477 down-regulated in the SLA group). The results were further validated via quantitative real-time polymerase chain reaction of 16 selected DEGs and were deemed highly reliable. The differences in growth rates between the two groups were attributed to the DEGs associated with carbohydrate metabolism, cysteine and methionine metabolism, and cardiac muscle contraction. Hex-t2, Fbp2, and Pepck were the most promising candidate genes to explain the differences in growth rate between SLA and SLB. These results provide valuable insights into fish growth traits and may aid in the identification of biomarkers for the establishment of selection models for S. lanzhouensis and other cultured fish species.

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Acknowledgements

The authors have no conflicts of interest to report. Wu X.D. and Lian Z.Q. conceived and designed the experiments. Xiao W. and Yu Z.X. performed the experiments. Xiao W. and Sai Q.Y. analyzed the data. Xiao W. and Wu J.P. wrote the manuscript. All authors read and approved the final manuscript. This study was supported by the Science and Technology Department of Ningxia (Grant No. 2017BN06) and the Ministry of Science and Technology of the People’s Republic of China (Grant No. 2018YFD0901202).

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Correspondence to Wei Xiao.

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Xiao, W., Lian, ZQ., Wu, JP. et al. De novo RNA sequencing for identification of growth-related genes in Silurus lanzhouensis muscle tissues. Fish Sci 88, 565–580 (2022). https://doi.org/10.1007/s12562-022-01598-x

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  • DOI: https://doi.org/10.1007/s12562-022-01598-x

Keywords

  • Growth-related genes
  • Muscle tissue
  • RNA-sequencing
  • Silurus lanzhouensis