Validation of Reference Genes for Real-Time PCR of Reproductive System in the Black Tiger Shrimp

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Leelatanawit, Rungnapa ^a   Klanchui, Amornpan ^a   Uawisetwathana, Umaporn ^a   Karoonuthaisiri, Nitsara ^a  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ACTIN; ELONGATION FACTOR 1ALPHA; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; RNA 18S; VITELLOGENIN;

ANIMAL TISSUE; ARTICLE; BETA ACTIN GENE; BIOINFORMATICS; CONTROLLED STUDY; DMC1 GENE; EF1 ALPHA GENE; FEMALE; GAPDH GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC STABILITY; GENITAL SYSTEM; HOUSEKEEPING GENE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; OVARY; PENAEUS MONODON; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA 18S GENE; TESTIS; VALIDATION PROCESS; VITELLOGENIN GENE;

ANIMALS; DECAPODA (CRUSTACEA); FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, ESSENTIAL; MALE; OVARY; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; REPRODUCTION; TESTIS;

MONODON; PENAEUS MONODON;

EID: 84871673742     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052677     Document Type: Article

References (70)

1. Jemiolo B, Trappe S, (2004) Single muscle fiber gene expression in human skeletal muscle: validation of internal control with exercise. Biochem Biophys Res Commun 320: 1043-1050.
2. Goidin D, Mamessier A, Staquet MJ, Schmitt D, Berthier-Vergnes O, (2001) Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Anal Biochem 295: 17-21.
3. Yang Y, Creer A, Jemiolo B, Trappe S, (2005) Time course of myogenic and metabolic gene expression in response to acute exercise in human skeletal muscle. J Appl Physiol 98: 1745-1752.
4. He JQ, Sandford AJ, Wang IM, Stepaniants S, Knight DA, et al. (2008) Selection of housekeeping genes for real-time PCR in atopic human bronchial epithelial cells. Eur Respir J 32: 755-762.
5. Foldager CB, Munir S, Ulrik-Vinther M, Soballe K, Bunger C, et al. (2009) Validation of suitable house keeping genes for hypoxia-cultured human chondrocytes. BMC Mol Biol 10: 94.
6. Filby AL, Tyler CR, (2007) Appropriate 'housekeeping' genes for use in expression profiling the effects of environmental estrogens in fish. BMC Mol Biol 8: 10.
7. Zhang Z, Hu J, (2007) Development and validation of endogenous reference genes for expression profiling of medaka (Oryzias latipes) exposed to endocrine disrupting chemicals by quantitative real-time RT-PCR. Toxicol Sci 95: 356-368.
8. Infante C, Asensio E, Canavate JP, Manchado M, (2008) Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Solea senegalensis Kaup): differential gene expression and thyroid hormones dependence during metamorphosis. BMC Mol Biol 9: 19.
9. McCurley AT, Callard GV, (2008) Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol Biol 9: 102.
10. Jain M, Nijhawan A, Tyagi AK, Khurana JP, (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651.
11. Jian B, Liu B, Bi Y, Hou W, Wu C, et al. (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
12. Carrillo-Casas EM, Hernandez-Castro R, Suarez-Guemes F, de la Pena-Moctezuma A, (2008) Selection of the internal control gene for real-time quantitative rt-PCR assays in temperature treated Leptospira. Curr Microbiol 56: 539-546.
13. Dhar AK, Bowers RM, Licon KS, Veazey G, Read B, (2009) Validation of reference genes for quantitative measurement of immune gene expression in shrimp. Mol Immunol 46: 1688-1695.
14. Pongsomboon S, Tang S, Boonda S, Aoki T, Hirono I, et al. (2008) Differentially expressed genes in Penaeus monodon hemocytes following infection with yellow head virus.
15. Zhou F, Jiang S, Huang J, Qiu L, Zhang D, et al. (2011) Molecular analysis of the QM gene from Penaeus monodon and its expression on the different ovarian stages of development. Molecular Biology Reports 38: 1921-1927.
16. Antony SP, Singh ISB, Sudheer NS, Vrinda S, Priyaja P, et al. (2011) Molecular characterization of a crustin-like antimicrobial peptide in the giant tiger shrimp, Penaeus monodon, and its expression profile in response to various immunostimulants and challenge with WSSV. Immunobiology 216: 184-194.
17. Somboonwiwat K, Supungul P, Rimphanitchayakit V, Aoki T, Hirono I, et al. (2006) Differentially expressed genes in hemocytes of Vibrio harveyi-challenged shrimp Penaeus monodon.
18. Leelatanawit R, Uawisetwathana U, Klinbunga S, Karoonuthaisiri N, (2011) A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon). BMC Mol Biol 12: 15.
19. Underwood DJ, Cowley JA, Sellars MJ, Barnes AC, van Hulten MCW, et al. (2010) Gill-associated virus and recombinant protein vaccination in Penaeus monodon. Aquaculture 308: 82-88.
20. Uawisetwathana U, Leelatanawit R, Klanchui A, Prommoon J, Klinbunga S, et al. (2011) Insights into eyestalk ablation mechanism to induce ovarian maturation in the black tiger shrimp. PLoS One 6: e24427.
21. Tharntada S, Ponprateep S, Somboonwiwat K, Liu H, Soderhall I, et al. (2009) Role of anti-lipopolysaccharide factor from the black tiger shrimp, Penaeus monodon, in protection from white spot syndrome virus infection. J Gen Virol 90: 1491-1498.
22. Luo T, Li F, Lei K, Xu X, (2007) Genomic organization, promoter characterization and expression profiles of an antiviral gene PmAV from the shrimp Penaeus monodon. Molecular Immunology 44: 1516-1523.
23. Arts JAJ, Cornelissen FHJ, Cijsouw T, Hermsen T, Savelkoul HFJ, et al. (2007) Molecular cloning and expression of a Toll receptor in the giant tiger shrimp, Penaeus monodon. Fish & Shellfish Immunology 23: 504-513.
24. Karoonuthaisiri N, Sittikankeaw K, Preechaphol R, Kalachikov S, Wongsurawat T, et al. (2009) ReproArray(GTS): a cDNA microarray for identification of reproduction-related genes in the giant tiger shrimp Penaeus monodon and characterization of a novel nuclear autoantigenic sperm protein (NASP) gene. Comp Biochem Physiol Part D Genomics Proteomics 4: 90-99.
25. Wongsurawat T, Leelatanawit R, Thamniemdee N, Uawisetwathana U, Karoonuthaisiri N, et al. (2010) Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). BMC Mol Biol 11: 55.
26. Leelatanawit R, Klinbunga S, Aoki T, Hirono I, Valyasevi R, et al. (2008) Suppression subtractive hybridization (SSH) for isolation and characterization of genes related to testicular development in the giant tiger shrimp Penaeus monodon. BMB Rep 41: 796-802.
27. Leelatanawit R, Sittikankeaw K, Yocawibun P, Klinbunga S, Roytrakul S, et al. (2009) Identification, characterization and expression of sex-related genes in testes of the giant tiger shrimp Penaeus monodon. Comp Biochem Physiol A Mol Integr Physiol 152: 66-76.
28. Buaklin A, Klinbunga S, Mensveta P (2011) Identification and expression analysis of the Broad-Complex core protein isoform 6 (BR-C Z6) gene in the giant tiger shrimp Penaeus monodon (Penaeidae: Decapoda).
29. Phiriyangkul P, Puengyam P, Jakobsen IB, Utarabhand P, (2007) Dynamics of vitellogenin mRNA expression during vitellogenesis in the banana shrimp Penaeus (Fenneropenaeus) merguiensis using real-time PCR. Mol Reprod Dev 74: 1198-1207.
30. Tsutsui N, Kawazoe I, Ohira T, Jasmani S, Yang WJ, et al. (2000) Molecular Characterization of a cDNA Encoding Vitellogenin and Its Expression in the Hepatopancreas and Ovary during Vitellogenesis in the Kuruma Prawn, Penaeus japonicus. Zool Sci 17: 651-660.
31. Dhar AK, Bowers RM, Licon KS, Veazey G, Read B, (2009) Validation of reference genes for quantitative measurement of immune gene expression in shrimp. Molecular Immunology 46: 1688-1695.
32. Cale JM, Millican DS, Itoh H, Magness RR, Bird IM, (1997) Pregnancy Induces an Increase in the Expression of Glyceraldehyde-3-Phosphate Dehydrogenase in Uterine Artery Endothelial Cells. Journal of the Society for Gynecologic Investigation 4: 284-292.
33. Puissant C, Bayat-Sarmadi M, Devinoy E, Houdebine L-M, (1994) Variation of transferrin mRNA concentration in the rabbit mammary gland during the pregnancy-lactation-weaning cycle and in cultured mammary cells. A comparison with the other major milk protein mRNAs. European Journal of Endocrinology 130: 522-529.
34. Calvo EL, Boucher C, Coulombe Z, Morisset J, (1997) Pancreatic GAPDH Gene Expression during Ontogeny and Acute Pancreatitis Induced by Caerulein. Biochemical and Biophysical Research Communications 235: 636-640.
35. Mansur NR, Meyer-Siegler K, Wurzer JC, Sirover MA, (1993) Cell cycle regulation of the glyceraldehyde3phosphate dehydrogenaseluracil DNA glycosylase gene in normal human cells. Nucleic Acids Research 21: 993-998.
36. Jain M, Nijhawan A, Tyagi AK, Khurana JP, (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochemical and Biophysical Research Communications 345: 646-651.
37. Filby A, Tyler C, (2007) Appropriate 'housekeeping' genes for use in expression profiling the effects of environmental estrogens in fish. BMC Molecular Biology 8: 10.
38. Huggett J, Dheda K, Bustin S, Zumla A, (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6: 279-284.
39. Radonić A, Thulke S, Mackay IM, Landt O, Siegert W, et al. (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochemical and Biophysical Research Communications 313: 856-862.
40. Deindl E, Boengler K, van Royen N, Schaper W, (2002) Differential expression of GAPDH and β-actin in growing collateral arteries. Molecular and Cellular Biochemistry 236: 139-146.
41. Spanakis E, (1993) Problems related to the interpretation of autoradiographic data on gene expression using common constitutive transcripts as controls. Nucleic Acids Research 21: 3809-3819.
42. Krüssel JS, Huang H-Y, Simón C, Behr B, Pape AR, et al. (1998) Single Blastomeres within Human Preimplantation Embryos Express Different Amounts of Messenger Ribonucleic Acid for β-Actin and Interleukin-1 Receptor Type I. Journal of Clinical Endocrinology & Metabolism. 83: 953-959.
43. Foss DL, Baarsch MJ, Murtaugh MP, (1998) Regulation of hypoxanthine phosphoribosyltransferase, glyceraldehyde-3-phosphate dehydrogenase and β-actin mRNA expression in porcine immune cells and tissues. Animal Biotechnology 9: 67-78.
44. Carlyle WC, Toher CA, Vandervelde JR, McDonald KM, Homans DC, et al. (1996) Changes inβ-actin mRNA Expression in Remodeling Canine Myocardium. Journal of Molecular and Cellular Cardiology 28: 53-63.
45. Sellars MJ, Vuocolo T, Leeton LA, Coman GJ, Degnan BM, et al. (2007) Real-time RT-PCR quantification of Kuruma shrimp transcripts: A comparison of relative and absolute quantification procedures. Journal of Biotechnology 129: 391-399.
46. Dirnhofer S, Berger C, Untergasser G, Geley S, Berger P, (1995) Human β-actin retropseudogenes interfere with RT-PCR. Trends in Genetics 11: 380-381.
47. Ingerslev H-C, Pettersen EF, Jakobsen RA, Petersen CB, Wergeland HI, (2006) Expression profiling and validation of reference gene candidates in immune relevant tissues and cells from Atlantic salmon (Salmo salar L.). Molecular Immunology 43: 1194-1201.
48. Olsvik P, Lie K, Jordal A-E, Nilsen T, Hordvik I, (2005) Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon. BMC Molecular Biology 6: 21.
49. Van Hiel M, Van Wielendaele P, Temmerman L, Van Soest S, Vuerinckx K, et al. (2009) Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions. BMC Molecular Biology 10: 56.
50. Infante C, Matsuoka MP, Asensio E, Canavate JP, Reith M, et al. (2008) Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR. BMC Mol Biol 9: 28.
51. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: RESEARCH0034.
52. Andersen CL, Jensen JL, Orntoft TF, (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250.
53. Kortner TM, Valen EC, Kortner H, Marjara IS, Krogdahl Å, et al. (2011) Candidate reference genes for quantitative real-time PCR (qPCR) assays during development of a diet-related enteropathy in Atlantic salmon (Salmo salar L.) and the potential pitfalls of uncritical use of normalization software tools. Aquaculture 318: 355-363.
54. Mehdi Khanlou K, Van Bockstaele E, (2012) A critique of widely used normalization software tools and an alternative method to identify reliable reference genes in red clover (Trifolium pratense; L.). Planta 236: 1381-1393.
55. Kajiura-Kobayashi H, Kobayashi T, Nagahama Y, (2005) Cloning of cDNAs and the differential expression of A-type cyclins and Dmc1 during spermatogenesis in the Japanese eel, a teleost fish. Dev Dyn 232: 1115-1123.
56. Habu T, Taki T, West A, Nishimune Y, Morita T, (1996) The mouse and human homologs of DMC1, the yeast meiosis-specific homologous recombination gene, have a common unique form of exon-skipped transcript in meiosis. Nucleic Acids Res 24: 470-477.
57. Yoshida K, Kondoh G, Matsuda Y, Habu T, Nishimune Y, et al. (1998) The mouse RecA-like gene Dmc1 is required for homologous chromosome synapsis during meiosis. Mol Cell 1: 707-718.
58. Ozaki Y, Miura C, Miura T, (2006) Molecular cloning and gene expression of Spo11 during spermatogenesis in the Japanese eel, Anguilla japonica. Comp Biochem Physiol B Biochem Mol Biol 143: 309-314.
59. Okutsu T, Kang B, Miwa M, Yoshizaki G, Maeno Y, et al. (2010) Molecular cloning and characterization of Dmc1, a gene involved in gametogenesis, from the whiteleg shrimp Litopenaeus vannamei. Fisheries Science 76: 961-969.
60. Takanami T, Sato S, Ishihara T, Katsura I, Takahashi H, et al. (1998) Characterization of a Caenorhabditis elegans recA-like gene Ce-rdh-1 involved in meiotic recombination. DNA Res 5: 373-377.
61. Ding Z-j, Wang T, Chong K, Bai S, (2001) Isolation and characterization of OsDMC1, the rice homologue of the yeast DMC1 gene essential for meiosis. Sexual Plant Reproduction 13: 285-288.
62. Doutriaux MP, Couteau F, Bergounioux C, White C, (1998) Isolation and characterisation of the RAD51 and DMC1 homologs from Arabidopsis thaliana. Mol Gen Genet 257: 283-291.
63. Bishop DK, Park D, Xu L, Kleckner N, (1992) DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 69: 439-456.
64. Stielow B, Krüger I, Diezko R, Finkernagel F, Gillemans N, et al. (2010) Epigenetic Silencing of Spermatocyte-Specific and Neuronal Genes by SUMO Modification of the Transcription Factor Sp3. PLoS Genet 6: e1001203.
65. Baillet A, Le Bouffant R, Volff JN, Luangpraseuth A, Poumerol E, et al. (2011) TOPAZ1, a Novel Germ Cell-Specific Expressed Gene Conserved during Evolution across Vertebrates. PLoS One 6: e26950.
66. Pfennig F, Kurth T, Meißner S, Standke A, Hoppe M, et al. (2012) The social status of the male Nile tilapia (Oreochromis niloticus) influences testis structure and gene expression. Reproduction 143: 71-84.
67. Zhang W, Wan H, Jiang H, Zhao Y, Zhang X, et al. (2011) A transcriptome analysis of mitten crab testes (Eriocheir sinensis). Genetics and Molecular Biology 34: 136-141.
68. Chu KH, Tam YK, Chung CK, Ng WL, (1993) Morphometric relationships and reproductive maturation of the shrimp, Metapenaeus ensis, from commercial catches in Hong Kong. Fisheries Research 18: 187-197.
69. Tan-Fermin JD, Pudadera RA, (1989) Ovarian maturation stages of the wild giant tiger prawn, Penaeus monodon Fabricius. Aquaculture 77: 229-242.
70. Kim YK, Tsutsui N, Kawazoe I, Okumura T, Kaneko T, et al. (2005) Localization and developmental expression of mRNA for cortical rod protein in kuruma prawn Marsupenaeus japonicus. Zoolog Sci 22: 675-680.