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Year 2022, , 176 - 182, 29.06.2022

Emin Ufuk Karakaş Ayşe Nur Pektaş , Şeyda Berk

https://doi.org/10.17776/csj.1069230
Cited By: 1

Abstract

References

  • [1] Hudson M.E., Sequencing breakthroughs for genomic ecology and evolutionary biology, Mol. Ecol. Resour., 8 (2008) 3-17.
  • [2] Li R., Xie W., Wang S., Wu Q., Yang N., Yang X., Pan H., Zhou X., Bai L., Xu B., Zhou X., Zhang Y., Reference gene selection for qRT-PCR analysis in the sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), PLoS One, 8 (2013) e53006.
  • [3] Lourenço A.P., Mackert A., Cristino A.d.S., Simões Z.L.P., Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR, Apidologie, 39 (2008) 372-385.
  • [4] Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., Speleman F., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome biology, 3 (2002) Research0034.
  • [5] Strube C., Buschbaum S., Wolken S., Schnieder T., Evaluation of reference genes for quantitative real-time PCR to investigate protein disulfide isomerase transcription pattern in the bovine lungworm Dictyocaulus viviparus, Gene, 425 (2008) 36-43.
  • [6] Guo J., Ling H., Wu Q., Xu L., Que Y., The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses, Scientific Reports, 4 (2014) 7042.
  • [7] Andersen C.L., Jensen J.L., Ørntoft T.F., 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 Research, 64 (2004) 5245-50.
  • [8] Van Hiel M.B., Van Wielendaele P., Temmerman L., Van Soest S., Vuerinckx K., Huybrechts R., Broeck J.V., Simonet G., Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions, BMC Mol Biol., 10 (2009) 56.
  • [9] Pitino M., Coleman A.D., Maffei M.E., Ridout C.J., Hogenhout S.A., Silencing of aphid genes by dsRNA feeding from plants, PLoS One, 6 (2011) e25709.
  • [10] Fu W., Xie W., Zhang Z., Wang S., Wu Q., Liu Y., Zhou X., Zhou X., Zhang Y., Exploring valid reference genes for quantitative real-time PCR analysis in Plutella xylostella (Lepidoptera: Plutellidae), Int. J. Biol. Sci., 9 (2013) 792-802.
  • [11] Berk S., and Pektas A., Selection and Validation of Reference Genes for Quantitative Real-time PCR in the Mealworm Beetle, Tenebrio molitorL. (Coleoptera: Tenebrionidae), IOSR-JAVS., 13 (2020) 44-50.
  • [12] Ladror D.T., Frey B.L., Scalf M., Levenstein M.E., Artymiuk J.M., Smith L.M., Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions, Biochemical and Biophysical Research Communications, 445 (2014) 535-41.
  • [13] Ponton F., Chapuis M.P., Pernice M., Sword G.A., Simpson S.J., Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster, J. Insect Physiol., 57 (2011) 840-50.
  • [14] Parker J.D., Parker K.M., Keller L., Molecular phylogenetic evidence for an extracellular Cu Zn superoxide dismutase gene in insects, Insect Molecular Biology, 13 (2004) 587-94.
  • [15] Rodrigues T.B., Khajuria C., Wang H., Matz N., Cunha Cardoso D., Valicente F.H., Zhou X., Siegfried B., Validation of reference housekeeping genes for gene expression studies in western corn rootworm (Diabrotica virgifera virgifera), PLoS One, 9 (2014) e109825.
  • [16] Lee P.D., Sladek R., Greenwood C.M., Hudson T.J., Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies, Genome Research, 12 (2002) 292-7.
  • [17] Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P., Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations, Biotechnology Letters, 26 (2004) 509-15.
  • [18] Silver N., Best S., Jiang J., Thein S.L.J.B.m.b., Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR, 7 (2006) 1-9.
  • [19] Pomés A., Arruda L.K., Investigating cockroach allergens: aiming to improve diagnosis and treatment of cockroach allergic patients, Methods (San Diego, Calif.), 66 (2014) 75-85.
  • [20] Wu H., Appel A.G., Hu X.P., Instar determination of Blaptica dubia (Blattodea: Blaberidae) using Gaussian mixture models, Annals of the Entomological Society of America, 106 (2013) 323-328.
  • [21] Zhang J., Zhang Y., Li J., Liu M., Liu Z., Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response, PLoS One, 11 (2016) e0155254.
  • [22] Shakeel M., Rodriguez A., Tahir U.B., Jin F., Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects, Biotechnology Letters, 40 (2018) 227-236.
  • [23] Lü J., Yang C., Zhang Y., Pan H., Selection of Reference Genes for the Normalization of RT-qPCR Data in Gene Expression Studies in Insects: A Systematic Review, Frontiers in Physiology, 9 (2018) 1560.
  • [24] Sang W., He L., Wang X.P., Zhu-Salzman K., Lei C.L., Evaluation of Reference Genes for RT-qPCR in Tribolium castaneum (Coleoptera: Tenebrionidae) Under UVB Stress, Environmental Entomology, 44 (2015) 418-25.
  • [25] Yang C., Pan H., Noland J.E., Zhang D., Zhang Z., Liu Y., Zhou X., Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae), Scientific Reports, 5 (2015) 18201.
  • [26] García-Reina A., Rodríguez-García M.J., Galián J., Validation of reference genes for quantitative real-time PCR in tiger beetles across sexes, body parts, sexual maturity and immune challenge, Scientific Reports, 8 (2018) 10743.
  • [27] Pan H., Yang X., Siegfried B.D., Zhou X., A Comprehensive Selection of Reference Genes for RT-qPCR Analysis in a Predatory Lady Beetle, Hippodamia convergens (Coleoptera: Coccinellidae), PLoS One, 10 (2015) e0125868.
  • [28] Altincicek B., Knorr E., Vilcinskas A., Beetle immunity: Identification of immune-inducible genes from the model insect Tribolium castaneum. Developmental & Comparative Immunology, 32 (2008) 585-595.
  • [29] Liang P., Guo Y., Zhou X., Gao X., Expression profiling in Bemisia tabaci under insecticide treatment: indicating the necessity for custom reference gene selection, PLoS One 9 (2014) e87514.
  • [30] Lu Y., Zheng X., Liang Q., Xu H., Yang Y., Tian J., He X., Lu Z., Evaluation and validation of reference genes for SYBR Green qRT-PCR normalization in Sesamia inferens (Lepidoptera: Noctuidae), J. Asia-Pac. Entomol., 18 (2015) 669-675.
  • [31] Yuan M., Lu Y., Zhu X., Wan H., Shakeel M., Zhan S., Jin B.R., Li J., Selection and evaluation of potential reference genes for gene expression analysis in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) using reverse-transcription quantitative PCR, PLoS One, 9 (2014) e86503.
  • [32] Jiang H.B., Liu Y.H., Tang P.A., Zhou A.W., Wang J.J., Validation of endogenous reference genes for insecticide-induced and developmental expression profiling of Liposcelis bostsrychophila (Psocoptera: Liposcelididae), Mol. Biol. Rep., 37 (2010) 1019-29.
  • [33] Teng X., Zhang Z., He G., Yang L., Li F., Validation of reference genes for quantitative expression analysis by real-time rt-PCR in four lepidopteran insects, J. Insect Sci., 12 (2012) 60.
  • [34] Yang C.,. Pan H, Noland J.E., Zhang D., Zhang Z., Liu Y., Zhou X., Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae), Scientific Reports, 5 (2015) 1-11.
  • [35] Zhang S., An S., Li Z., Wu F., Yang Q., Liu Y., Cao J., Zhang H., Zhang Q., Liu X., Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Helicoverpa armigera (Lepidoptera: Noctuidae), Gene, 555 (2015) 393-402.
  • [36] An X.-k., Hou M.-l., Liu Y.-d., Reference gene selection and evaluation for gene expression studies using qRT-PCR in the white-backed planthopper, Sogatella furcifera (Hemiptera: Delphacidae), J. Econ. Entomol., 109 (2016) 879-886.
  • [37] Zhai Y., Lin Q., Zhou X., Zhang X., Liu T., Yu Y., Identification and validation of reference genes for quantitative real-time PCR in Drosophila suzukii (Diptera: Drosophilidae), PLoS One, 9 (2014) e106800.
  • [38] Mamidala P., Rajarapu S.P., Jones S.C., Mittapalli O., Identification and validation of reference genes for quantitative real-time polymerase chain reaction in Cimex lectularius, Journal of Medical Entomology, 48 (2011) 947-51.
  • [39] Hornáková D., Matousková P., Kindl J., Valterová I., Pichová I., Selection of reference genes for real-time polymerase chain reaction analysis in tissues from Bombus terrestris and Bombus lucorum of different ages, Analytical Biochemistry, 397 (2010) 118-20.
  • [40] Marchal E., Hult E.F., Huang J., Tobe S.S., Sequencing and validation of housekeeping genes for quantitative real-time PCR during the gonadotrophic cycle of Diploptera punctata, BMC Research Notes, 6 (2013) 237.

Selection and Validation of Potential Reference Genes for Quantitative Real-Time PCR Analysis in Blaptica Dubia (Serville, 1838) (Blattidae, Blaberidae)

Year 2022, , 176 - 182, 29.06.2022

Emin Ufuk Karakaş Ayşe Nur Pektaş , Şeyda Berk

https://doi.org/10.17776/csj.1069230
Cited By: 1

Abstract

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an effective, reproducible, and dependable method for evaluating and targeting expression of genes. It is very important to normalize according to stably expressed housekeeping genes in order to facilitating gene expression studies and to acquire exact and meaningful results. The purpose of this study was to identify and validate six housekeeping genes (GADPH, RPS18, α-TUB, EF1α, ArgK and ACTB) in adults of cockroach species Blaptica dubia employing five different algorithms (geNorm, Bestkeeper, Normfinder, ΔCt method and RefFinder) to assess putative housekeeping gene expression stability. Our study also showed that the geNorm, Normfinder ΔCt method and RefFinder algorithms identified GADPH as the most stable housekeeping gene in B. dubia adults. Additioanlly, RPS18 was suggested as the most stable gene by GeNorm and BestKeeeper. ACTB has been shown to be by far the least stable of all algorithms. In addition, since there are few validation studies for reference genes in cockroaches in the literature, it is considered that it would be beneficial to increase the number of studies related with RT-qPCR on the reference genes validation under biotic and abiotic conditions in cockroaches.

Keywords

Blaptica dubia RT-qPCR Reference genes Validation Normalization.

References

  • [1] Hudson M.E., Sequencing breakthroughs for genomic ecology and evolutionary biology, Mol. Ecol. Resour., 8 (2008) 3-17.
  • [2] Li R., Xie W., Wang S., Wu Q., Yang N., Yang X., Pan H., Zhou X., Bai L., Xu B., Zhou X., Zhang Y., Reference gene selection for qRT-PCR analysis in the sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), PLoS One, 8 (2013) e53006.
  • [3] Lourenço A.P., Mackert A., Cristino A.d.S., Simões Z.L.P., Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR, Apidologie, 39 (2008) 372-385.
  • [4] Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., Speleman F., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome biology, 3 (2002) Research0034.
  • [5] Strube C., Buschbaum S., Wolken S., Schnieder T., Evaluation of reference genes for quantitative real-time PCR to investigate protein disulfide isomerase transcription pattern in the bovine lungworm Dictyocaulus viviparus, Gene, 425 (2008) 36-43.
  • [6] Guo J., Ling H., Wu Q., Xu L., Que Y., The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses, Scientific Reports, 4 (2014) 7042.
  • [7] Andersen C.L., Jensen J.L., Ørntoft T.F., 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 Research, 64 (2004) 5245-50.
  • [8] Van Hiel M.B., Van Wielendaele P., Temmerman L., Van Soest S., Vuerinckx K., Huybrechts R., Broeck J.V., Simonet G., Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions, BMC Mol Biol., 10 (2009) 56.
  • [9] Pitino M., Coleman A.D., Maffei M.E., Ridout C.J., Hogenhout S.A., Silencing of aphid genes by dsRNA feeding from plants, PLoS One, 6 (2011) e25709.
  • [10] Fu W., Xie W., Zhang Z., Wang S., Wu Q., Liu Y., Zhou X., Zhou X., Zhang Y., Exploring valid reference genes for quantitative real-time PCR analysis in Plutella xylostella (Lepidoptera: Plutellidae), Int. J. Biol. Sci., 9 (2013) 792-802.
  • [11] Berk S., and Pektas A., Selection and Validation of Reference Genes for Quantitative Real-time PCR in the Mealworm Beetle, Tenebrio molitorL. (Coleoptera: Tenebrionidae), IOSR-JAVS., 13 (2020) 44-50.
  • [12] Ladror D.T., Frey B.L., Scalf M., Levenstein M.E., Artymiuk J.M., Smith L.M., Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions, Biochemical and Biophysical Research Communications, 445 (2014) 535-41.
  • [13] Ponton F., Chapuis M.P., Pernice M., Sword G.A., Simpson S.J., Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster, J. Insect Physiol., 57 (2011) 840-50.
  • [14] Parker J.D., Parker K.M., Keller L., Molecular phylogenetic evidence for an extracellular Cu Zn superoxide dismutase gene in insects, Insect Molecular Biology, 13 (2004) 587-94.
  • [15] Rodrigues T.B., Khajuria C., Wang H., Matz N., Cunha Cardoso D., Valicente F.H., Zhou X., Siegfried B., Validation of reference housekeeping genes for gene expression studies in western corn rootworm (Diabrotica virgifera virgifera), PLoS One, 9 (2014) e109825.
  • [16] Lee P.D., Sladek R., Greenwood C.M., Hudson T.J., Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies, Genome Research, 12 (2002) 292-7.
  • [17] Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P., Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations, Biotechnology Letters, 26 (2004) 509-15.
  • [18] Silver N., Best S., Jiang J., Thein S.L.J.B.m.b., Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR, 7 (2006) 1-9.
  • [19] Pomés A., Arruda L.K., Investigating cockroach allergens: aiming to improve diagnosis and treatment of cockroach allergic patients, Methods (San Diego, Calif.), 66 (2014) 75-85.
  • [20] Wu H., Appel A.G., Hu X.P., Instar determination of Blaptica dubia (Blattodea: Blaberidae) using Gaussian mixture models, Annals of the Entomological Society of America, 106 (2013) 323-328.
  • [21] Zhang J., Zhang Y., Li J., Liu M., Liu Z., Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response, PLoS One, 11 (2016) e0155254.
  • [22] Shakeel M., Rodriguez A., Tahir U.B., Jin F., Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects, Biotechnology Letters, 40 (2018) 227-236.
  • [23] Lü J., Yang C., Zhang Y., Pan H., Selection of Reference Genes for the Normalization of RT-qPCR Data in Gene Expression Studies in Insects: A Systematic Review, Frontiers in Physiology, 9 (2018) 1560.
  • [24] Sang W., He L., Wang X.P., Zhu-Salzman K., Lei C.L., Evaluation of Reference Genes for RT-qPCR in Tribolium castaneum (Coleoptera: Tenebrionidae) Under UVB Stress, Environmental Entomology, 44 (2015) 418-25.
  • [25] Yang C., Pan H., Noland J.E., Zhang D., Zhang Z., Liu Y., Zhou X., Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae), Scientific Reports, 5 (2015) 18201.
  • [26] García-Reina A., Rodríguez-García M.J., Galián J., Validation of reference genes for quantitative real-time PCR in tiger beetles across sexes, body parts, sexual maturity and immune challenge, Scientific Reports, 8 (2018) 10743.
  • [27] Pan H., Yang X., Siegfried B.D., Zhou X., A Comprehensive Selection of Reference Genes for RT-qPCR Analysis in a Predatory Lady Beetle, Hippodamia convergens (Coleoptera: Coccinellidae), PLoS One, 10 (2015) e0125868.
  • [28] Altincicek B., Knorr E., Vilcinskas A., Beetle immunity: Identification of immune-inducible genes from the model insect Tribolium castaneum. Developmental & Comparative Immunology, 32 (2008) 585-595.
  • [29] Liang P., Guo Y., Zhou X., Gao X., Expression profiling in Bemisia tabaci under insecticide treatment: indicating the necessity for custom reference gene selection, PLoS One 9 (2014) e87514.
  • [30] Lu Y., Zheng X., Liang Q., Xu H., Yang Y., Tian J., He X., Lu Z., Evaluation and validation of reference genes for SYBR Green qRT-PCR normalization in Sesamia inferens (Lepidoptera: Noctuidae), J. Asia-Pac. Entomol., 18 (2015) 669-675.
  • [31] Yuan M., Lu Y., Zhu X., Wan H., Shakeel M., Zhan S., Jin B.R., Li J., Selection and evaluation of potential reference genes for gene expression analysis in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) using reverse-transcription quantitative PCR, PLoS One, 9 (2014) e86503.
  • [32] Jiang H.B., Liu Y.H., Tang P.A., Zhou A.W., Wang J.J., Validation of endogenous reference genes for insecticide-induced and developmental expression profiling of Liposcelis bostsrychophila (Psocoptera: Liposcelididae), Mol. Biol. Rep., 37 (2010) 1019-29.
  • [33] Teng X., Zhang Z., He G., Yang L., Li F., Validation of reference genes for quantitative expression analysis by real-time rt-PCR in four lepidopteran insects, J. Insect Sci., 12 (2012) 60.
  • [34] Yang C.,. Pan H, Noland J.E., Zhang D., Zhang Z., Liu Y., Zhou X., Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae), Scientific Reports, 5 (2015) 1-11.
  • [35] Zhang S., An S., Li Z., Wu F., Yang Q., Liu Y., Cao J., Zhang H., Zhang Q., Liu X., Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Helicoverpa armigera (Lepidoptera: Noctuidae), Gene, 555 (2015) 393-402.
  • [36] An X.-k., Hou M.-l., Liu Y.-d., Reference gene selection and evaluation for gene expression studies using qRT-PCR in the white-backed planthopper, Sogatella furcifera (Hemiptera: Delphacidae), J. Econ. Entomol., 109 (2016) 879-886.
  • [37] Zhai Y., Lin Q., Zhou X., Zhang X., Liu T., Yu Y., Identification and validation of reference genes for quantitative real-time PCR in Drosophila suzukii (Diptera: Drosophilidae), PLoS One, 9 (2014) e106800.
  • [38] Mamidala P., Rajarapu S.P., Jones S.C., Mittapalli O., Identification and validation of reference genes for quantitative real-time polymerase chain reaction in Cimex lectularius, Journal of Medical Entomology, 48 (2011) 947-51.
  • [39] Hornáková D., Matousková P., Kindl J., Valterová I., Pichová I., Selection of reference genes for real-time polymerase chain reaction analysis in tissues from Bombus terrestris and Bombus lucorum of different ages, Analytical Biochemistry, 397 (2010) 118-20.
  • [40] Marchal E., Hult E.F., Huang J., Tobe S.S., Sequencing and validation of housekeeping genes for quantitative real-time PCR during the gonadotrophic cycle of Diploptera punctata, BMC Research Notes, 6 (2013) 237.
There are 40 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Natural Sciences
Authors

Emin Ufuk Karakaş 0000-0001-5813-5678

Ayşe Nur Pektaş 0000-0001-5621-2844

Şeyda Berk 0000-0003-4687-0223

Publication Date June 29, 2022
Submission Date February 7, 2022
Acceptance Date June 3, 2022
Published in Issue Year 2022

Cite

APA Karakaş, E. U., Pektaş, A. N., & Berk, Ş. (2022). Selection and Validation of Potential Reference Genes for Quantitative Real-Time PCR Analysis in Blaptica Dubia (Serville, 1838) (Blattidae, Blaberidae). Cumhuriyet Science Journal, 43(2), 176-182. https://doi.org/10.17776/csj.1069230

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