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Determination of suitable housekeeping genes for normalization of quantitative real time PCR analysis of Avicennia marina under crude oil treatment

Document Type : Original Manuscript

Authors

1 Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

2 Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

3 Department of Plant Biology and Center of Excellence in Phylogeny of Living Organisms in Iran, 3. School of Biology, College of Science, University of Tehran, Iran

4 School of Biology, College of Science, University of Tehran, Iran Iranian National Institute for Oceanography and Atmospheric Science, Tehran, Iran

Abstract

Gene expression studies could provide insight into the physiological mechanisms and strategies used by plants under stress conditions. Selection of suitable internal control gene(s) is essential to accurately assess gene expression levels. For the mangrove plant, Avicennia marina, reliable reference genes to normalize real-time quantitative PCR data has not been previously investigated. In this study, the expression stabilities of four candidate reference genes [Actin 2 (ACT2),Serine/threonine-protein phosphatase 2A subunit A3 (PP2AA3),TIP-Like (TIP), polyubiquitin 10 (UBQ)] were determined in leaves and roots of A. marina treated by different level of oils contamination . Three software programs (Bestkeeper, NormFinder and geNorm) were employed to analyze and rank the tested genes. Results showed that ACT2 was the most suitable reference gene in A. marina and the combination of two or three genes was recommended for greater accuracy. Identification of A. marina reference genes in a wide range of experimental samples will provide a useful reference in future gene expression studies in this species, particularly involving similar stresses.

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References
Czechowski, T., Stitt, M., Altmann, T., Udvardi, M.K. and Scheible, W.-R. 2005. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiology. 139(1): 5-17.
Die, J.V., Román, B., Nadal, S. and González-Verdejo, C.I. 2010. Evaluation of candidate reference genes for expression studies in Pisum sativum under different experimental conditions. Planta. 232(1): 145-153.
Ebrahimi-Sirizi, Z. and Riyahi-Bakhtiyari, A. 2013. Petroleum pollution in mangrove forests sediments from Qeshm Island and Khamir Port—Persian Gulf, Iran. Environmental Monitoring and Assessment. 185(5): 4019-4032.
Heid, C.A., Stevens, J., Livak, K.J. and Williams, P.M. 1996. Real time quantitative PCR. Genome Research. 6(10): 986-994.
Higuchi, R., Fockler, C., Dollinger, G. and Watson, R. 1993. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology. 11: 1026-1030.
Hong, S.M., Bahn, S.C., Lyu, A., Jung, H.S. and Ahn, J.H. 2010. Identification and testing of superior reference genes for a starting pool of transcript normalization in Arabidopsis. Plant and Cell Physiology. 51(10): 1694-1706.
Hu, R., Fan, C., Li, H., Zhang, Q. and Fu, Y.-F. 2009. Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Molecular Biology. 10(1): 1.
Kong, Q., Yuan, J., Gao, L., Zhao, S., Jiang, W., Huang, Y. and Bie, Z. 2014a. Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon. PloS one. 9(2): e90612.
Kong, Q., Yuan, J., Niu, P., Xie, J., Jiang, W., Huang, Y. and Bie, Z. 2014b. Screening suitable reference genes for normalization in reverse transcription quantitative real-time PCR analysis in melon. PloS one. 9(1): e87197.
Kozera, B. and Rapacz, M. 2013. Reference genes in real-time PCR. Journal of Applied Genetics. 54(4): 391-406.
 
Kulcheski, F.R., Marcelino-Guimaraes, F.C., Nepomuceno, A.L., Abdelnoor, R.V. and Margis, R. 2010. The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Analytical Biochemistry. 406(2): 185-192.
Li, X.-S., Yang, H.-L., Zhang, D.-Y., Zhang, Y.-M. and Wood, A.J. 2012. Reference gene selection in the desert plant Eremosparton songoricum. International journal of molecular sciences. 13(6): 6944-6963.
Lilly, S., Drummond, R., Pearson, M. and MacDiarmid, R. 2011. Identification and validation of reference genes for normalization of transcripts from virus-infected Arabidopsis thaliana. Molecular Plant-Microbe Interactions. 24(3): 294-304.
Løvdal, T. and Lillo, C. 2009. Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Analytical Biochemistry. 387(2): 238-242.
Peng, Y.-L., Wang, Y.-S. and Gu, J.-D. 2015. Identification of suitable reference genes in mangrove Aegiceras corniculatum under abiotic stresses. Ecotoxicology. 24(7-8): 1714-1721.
Ramakers, C., Ruijter, J.M., Deprez, R.H.L. and Moorman, A.F. 2003. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters. 339(1): 62-66.
Rashvand, S. and Sadeghi, S.M. 2014. Distribution, Characteristics and Economic Importance of Mangrove Forests in Iran. Mangrove Ecosystems of Asia. Springer. pp. 95-126.
Remans, T., Smeets, K., Opdenakker, K., Mathijsen, D., Vangronsveld, J. and Cuypers, A. 2008. Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta. 227(6): 1343-1349.
Ruijter, J., Ramakers, C., Hoogaars, W., Karlen, Y., Bakker, O., Van den Hoff, M. and Moorman, A. 2009. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Research. 37(6): e45-e45.
Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270(5235): 467.
Shivhare, R., Lata, C. 2016. Selection of suitable reference genes for assessing gene expression in pearl millet under different abiotic stresses and their combinations. Scientific Reports. 7: 40290 DOI: 10.1038/srep40290
Suzuki, T., Higgins, P. and Crawford, D. 2000. Control selection for RNA quantitation. BioTechniques. 29(2): 332-337.
Thellin, O., Zorzi, W., Lakaye, B., De Borman, B., Coumans, B., Hennen, G., Grisar, T., Igout, A. and Heinen, E. 1999. Housekeeping genes as internal standards: use and limits. Journal of Biotechnology. 75(2): 291-295.
Tian, C., Jiang, Q., Wang, F., Wang, G.-L., Xu, Z.-S. and Xiong, A.-S. 2015. Selection of suitable reference genes for qPCR normalization under abiotic stresses and hormone stimuli in carrot leaves. PloS one. 10(2): e0117569.
van Bochove, J., Sullivan, E. and Nakamura, T. 2014. The importance of mangroves to people: A call to action. United Nations Environment Programme.
Wang, H., Wang, J., Jiang, J., Chen, S., Guan, Z., Liao, Y. and Chen, F. 2014. Reference genes for normalizing transcription in diploid and tetraploid Arabidopsis. Scientific reports. 4: 6781.
Wang, X., Liu, Y. and Yang, P. 2012. Proteomic studies of the abiotic stresses response in model moss–Physcomitrella patens. Frontiers in plant science. 3: 258.
Yang, Y., Hou, S., Cui, G., Chen, S., Wei, J. and Huang, L. 2010. Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza. Molecular Biology Reports. 37(1): 507-513
 
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Journal of Marine Science and Technology
Volume 17, Issue 4 - Serial Number 4
March 2019
Pages 58-69
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