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Research Article

volume 53 issue 9 (september 2019) : 1156-1161,   Doi: 10.18805/ijar.B-941

De novo transcriptome analysis of differentially expressed genes in the liver of pampus argenteus under temperature stress

Z
Zhaohong Shi
L
Lei Liu
Q
Quanxin Gao
S
Shiming Peng
Y
Yanfeng Yue
1<div style="text-align: justify;">Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 200 090, Shanghai, China.</div>
Cite article:- Shi Zhaohong, Liu Lei, Gao Quanxin, Peng Shiming, Yue Yanfeng (2018). De novo transcriptome analysis of differentially expressed genes in the liver of pampus argenteus under temperature stress. Indian Journal of Animal Research. 53(9): 1156-1161. doi: 10.18805/ijar.B-941.

ABSTRACT

Pampus argenteus is an aquatic cold-blooded animal, and its growth and survival are greatly affected by ambient temperature. During aquaculture, a sudden change in water temperature may be caused by climate change or other human factors, resulting in acute temperature stress. In this study, de novo transcriptome sequencing technology was used to analyze changes in the gene expressions in the liver of P. argenteus under temperature stress to understand the mechanisms of temperature regulation in P. argenteus. The results showed that 72447398, 69534310, 63698204, 78876728 and 53969050 clean reads were obtained from four cDNA libraries (A: 27°C (control group), B: 22°C and 6 h, C: 32°C and 6 h, D: 22°C and 12 h, E: 32°C and 12 h) of the P. argenteus by Illumina sequencing technology. In A\B, A\C, A\D and A\E pairwise comparison, 353, 431, 1303 and 343 differentially expressed genes (DEGs) were detected, respectively. Of these genes, 67 genes were identified among all the pairwise comparisons as the common DEGs. Four genes related to metabolic adaption to temperature were randomly selected to validate the DEGs results by real time PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated some vital genes and pathways associated with metabolism in response to temperature challenge. These results will help us to understand the molecular mechanism underlying temperature regulation in P. argenteus and provide a theoretical basis for the study of related molecular mechanisms in fish under temperature stress.

REFERENCES

  1. Alagna, F., D’Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., et al. (2009). Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics, 10: 399-399.
  2. Banerjee, S., Mitra, T., Purohit, G.K., Mohanty, S. and Mohanty, B.P. (2015). Immunomodulatory effect of arsenic on cytokine and HSP gene expression in Labeo rohita fingerlings. Fish Shellfish Immunol, 44: 43-9.
  3. Barakat, A., DiLoreto, D.S., Zhang, Y., Smith, C., Baier, K., Powell, W.A., Wheeler, N., et al. (2009). Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol, 9: 51.
  4. Chen, H., Chen, X., Chai, X., Qiu, Y., Gong, C., Zhang, Z., Wang, T., Zhang, Y., Li, J. and Wang, A. (2015). Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq. Biochemical and Biophysical Research Communications, 464: 768-773.
  5. Choi, S., Hwang, M.S., Im, S., Kim, N., Jeong, W.-J., Park, E.-J., Gong, Y.-G. and Choi, D.-W. (2013). Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions. Journal of Applied Phycology, 25: 1237-1246.
  6. Diaz, N.Piferrer, F. (2015). Lasting effects of early exposure to temperature on the gonadal transcriptome at the time of sex differentiation in the European sea bass, a fish with mixed genetic and environmental sex determination. BMC Genomics, 16: 679.
  7. Hu, J., You, F., Wang, Q., Weng, S., Liu, H., Wang, L., Zhang, P.J. and Tan, X. (2014). Transcriptional responses of olive flounder (Paralichthys olivaceus) to low temperature. PLoS One, 9: e108582.
  8. Imsland, A.K., Schram, E., Roth, B., Schelvis-Smit, R. and Kloet, K. (2007). Improving growth in juvenile turbot (Scophthalmus maximus Rafinesque) by rearing fish in switched temperature regimes. Aquaculture International, 15: 403-407.
  9. Jesus, Tiago F., Grosso, Ana R., Almeida-Val, V.M.F. and Coelho, M.M. (2016). Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress. Journal of Thermal Biology, 55: 54-61.
  10. Kocan, R., Hershberger, P., Sanders, G. and Winton, J. (2009). Effects of temperature on disease progression and swimming stamina in Ichthyophonus-infected rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis, 32: 835-43.
  11. Li, B., Fillmore, N., Bai, Y., Collins, M., Thomson, J.A., Stewart, R. and Dewey, C.N. (2014). Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology, 15: 1-21.
  12. Li, Y., Gao, T. and Song, N. (2016). The complete mitogenome of Pampus argenteus (Perciformes: Stromateidae). Mitochondrial DNA A DNA Mapp Seq Anal, 27: 684-5.
  13. Palstra, A.P., Beltran, S., Burgerhout, E., Brittijn, S.A., Magnoni, L.J., Henkel, C.V., et al. (2013). Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One, 8: e53171.
  14. Person-Le Ruyet, J., Buchet, V., Vincent, B., Le Delliou, H. and Quéméner, L. (2006). Effects of temperature on the growth of pollack (Pollachius pollachius) juveniles. Aquaculture, 251: 340-345.
  15. Podolak-Popinigis, J., Gornikiewicz, B., Ronowicz, A. and Sachadyn, P. (2015). Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse. BMC Genomics, 16: 926.
  16. Qian, B.Xue, L. (2016). Liver transcriptome sequencing and de novo annotation of the large yellow croaker (Larimichthy crocea) under heat and cold stress. Mar Genomics, 25: 95-102.
  17. Stewart, M.J., Stewart, P. and Rivera-Posada, J. (2015). De novo assembly of the transcriptome of Acanthaster planci testes. Molecular Ecology Resources, 15: 953-966.
  18. Sun, F., Peatman, E., Li, C., Liu, S., Jiang, Y., Zhou, Z. and Liu, Z. (2012). Transcriptomic signatures of attachment, NF-kappaB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Dev Comp Immunol, 38: 169-80.
  19. Sun, P., Yin, F., Shi, Z. and Peng, S. (2013). Genetic structure of silver pomfret (Pampus argenteus (Euphrasen, 1788)) in the Arabian Sea, Bay of Bengal, and South China Sea as indicated by mitochondrial COI gene sequences. Journal of Applied Ichthyology, 29: 733-737.
  20. Szövényi, P., Perroud, P.-F., Symeonidi, A., Stevenson, S., Quatrano, R.S., Rensing, S.A., et al. (2015). De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome. Molecular Ecology Resources, 15: 203-215.
  21. Tan, G.-F., Wang, F., Li, M.-Y., Wang, G.-L., Jiang, Q. and Xiong, A.-S. (2014). De novo assembly and transcriptome characterization: novel insights into the temperature stress in Cryptotaenia japonica Hassk. Acta Physiologiae Plantarum, 37: 1-12.
  22. Vesterlund, L., Jiao, H., Unneberg, P., Hovatta, O. and Kere, J. (2011). The zebrafish transcriptome during early development. BMC Developmental Biology, 11: 1-18.
  23. Xiang, L.X., He, D., Dong, W.R., Zhang, Y.W. and Shao, J.Z. (2010). Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics, 11: 472. 
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Indian Journal of Animal Research
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    Research Article

    volume 53 issue 9 (september 2019) : 1156-1161,   Doi: 10.18805/ijar.B-941

    De novo transcriptome analysis of differentially expressed genes in the liver of pampus argenteus under temperature stress

    Z
    Zhaohong Shi
    L
    Lei Liu
    Q
    Quanxin Gao
    S
    Shiming Peng
    Y
    Yanfeng Yue
    1<div style="text-align: justify;">Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 200 090, Shanghai, China.</div>
    Cite article:- Shi Zhaohong, Liu Lei, Gao Quanxin, Peng Shiming, Yue Yanfeng (2018). De novo transcriptome analysis of differentially expressed genes in the liver of pampus argenteus under temperature stress. Indian Journal of Animal Research. 53(9): 1156-1161. doi: 10.18805/ijar.B-941.

    ABSTRACT

    Pampus argenteus is an aquatic cold-blooded animal, and its growth and survival are greatly affected by ambient temperature. During aquaculture, a sudden change in water temperature may be caused by climate change or other human factors, resulting in acute temperature stress. In this study, de novo transcriptome sequencing technology was used to analyze changes in the gene expressions in the liver of P. argenteus under temperature stress to understand the mechanisms of temperature regulation in P. argenteus. The results showed that 72447398, 69534310, 63698204, 78876728 and 53969050 clean reads were obtained from four cDNA libraries (A: 27°C (control group), B: 22°C and 6 h, C: 32°C and 6 h, D: 22°C and 12 h, E: 32°C and 12 h) of the P. argenteus by Illumina sequencing technology. In A\B, A\C, A\D and A\E pairwise comparison, 353, 431, 1303 and 343 differentially expressed genes (DEGs) were detected, respectively. Of these genes, 67 genes were identified among all the pairwise comparisons as the common DEGs. Four genes related to metabolic adaption to temperature were randomly selected to validate the DEGs results by real time PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated some vital genes and pathways associated with metabolism in response to temperature challenge. These results will help us to understand the molecular mechanism underlying temperature regulation in P. argenteus and provide a theoretical basis for the study of related molecular mechanisms in fish under temperature stress.

    REFERENCES

    1. Alagna, F., D’Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., et al. (2009). Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics, 10: 399-399.
    2. Banerjee, S., Mitra, T., Purohit, G.K., Mohanty, S. and Mohanty, B.P. (2015). Immunomodulatory effect of arsenic on cytokine and HSP gene expression in Labeo rohita fingerlings. Fish Shellfish Immunol, 44: 43-9.
    3. Barakat, A., DiLoreto, D.S., Zhang, Y., Smith, C., Baier, K., Powell, W.A., Wheeler, N., et al. (2009). Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol, 9: 51.
    4. Chen, H., Chen, X., Chai, X., Qiu, Y., Gong, C., Zhang, Z., Wang, T., Zhang, Y., Li, J. and Wang, A. (2015). Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq. Biochemical and Biophysical Research Communications, 464: 768-773.
    5. Choi, S., Hwang, M.S., Im, S., Kim, N., Jeong, W.-J., Park, E.-J., Gong, Y.-G. and Choi, D.-W. (2013). Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions. Journal of Applied Phycology, 25: 1237-1246.
    6. Diaz, N.Piferrer, F. (2015). Lasting effects of early exposure to temperature on the gonadal transcriptome at the time of sex differentiation in the European sea bass, a fish with mixed genetic and environmental sex determination. BMC Genomics, 16: 679.
    7. Hu, J., You, F., Wang, Q., Weng, S., Liu, H., Wang, L., Zhang, P.J. and Tan, X. (2014). Transcriptional responses of olive flounder (Paralichthys olivaceus) to low temperature. PLoS One, 9: e108582.
    8. Imsland, A.K., Schram, E., Roth, B., Schelvis-Smit, R. and Kloet, K. (2007). Improving growth in juvenile turbot (Scophthalmus maximus Rafinesque) by rearing fish in switched temperature regimes. Aquaculture International, 15: 403-407.
    9. Jesus, Tiago F., Grosso, Ana R., Almeida-Val, V.M.F. and Coelho, M.M. (2016). Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress. Journal of Thermal Biology, 55: 54-61.
    10. Kocan, R., Hershberger, P., Sanders, G. and Winton, J. (2009). Effects of temperature on disease progression and swimming stamina in Ichthyophonus-infected rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis, 32: 835-43.
    11. Li, B., Fillmore, N., Bai, Y., Collins, M., Thomson, J.A., Stewart, R. and Dewey, C.N. (2014). Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology, 15: 1-21.
    12. Li, Y., Gao, T. and Song, N. (2016). The complete mitogenome of Pampus argenteus (Perciformes: Stromateidae). Mitochondrial DNA A DNA Mapp Seq Anal, 27: 684-5.
    13. Palstra, A.P., Beltran, S., Burgerhout, E., Brittijn, S.A., Magnoni, L.J., Henkel, C.V., et al. (2013). Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One, 8: e53171.
    14. Person-Le Ruyet, J., Buchet, V., Vincent, B., Le Delliou, H. and Quéméner, L. (2006). Effects of temperature on the growth of pollack (Pollachius pollachius) juveniles. Aquaculture, 251: 340-345.
    15. Podolak-Popinigis, J., Gornikiewicz, B., Ronowicz, A. and Sachadyn, P. (2015). Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse. BMC Genomics, 16: 926.
    16. Qian, B.Xue, L. (2016). Liver transcriptome sequencing and de novo annotation of the large yellow croaker (Larimichthy crocea) under heat and cold stress. Mar Genomics, 25: 95-102.
    17. Stewart, M.J., Stewart, P. and Rivera-Posada, J. (2015). De novo assembly of the transcriptome of Acanthaster planci testes. Molecular Ecology Resources, 15: 953-966.
    18. Sun, F., Peatman, E., Li, C., Liu, S., Jiang, Y., Zhou, Z. and Liu, Z. (2012). Transcriptomic signatures of attachment, NF-kappaB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Dev Comp Immunol, 38: 169-80.
    19. Sun, P., Yin, F., Shi, Z. and Peng, S. (2013). Genetic structure of silver pomfret (Pampus argenteus (Euphrasen, 1788)) in the Arabian Sea, Bay of Bengal, and South China Sea as indicated by mitochondrial COI gene sequences. Journal of Applied Ichthyology, 29: 733-737.
    20. Szövényi, P., Perroud, P.-F., Symeonidi, A., Stevenson, S., Quatrano, R.S., Rensing, S.A., et al. (2015). De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome. Molecular Ecology Resources, 15: 203-215.
    21. Tan, G.-F., Wang, F., Li, M.-Y., Wang, G.-L., Jiang, Q. and Xiong, A.-S. (2014). De novo assembly and transcriptome characterization: novel insights into the temperature stress in Cryptotaenia japonica Hassk. Acta Physiologiae Plantarum, 37: 1-12.
    22. Vesterlund, L., Jiao, H., Unneberg, P., Hovatta, O. and Kere, J. (2011). The zebrafish transcriptome during early development. BMC Developmental Biology, 11: 1-18.
    23. Xiang, L.X., He, D., Dong, W.R., Zhang, Y.W. and Shao, J.Z. (2010). Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics, 11: 472. 
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