Identifying optimal reference genes for gene expression studies in Eurasian spruce bark beetle, Ips typographus (Coleoptera: Curculionidae: Scolytinae)

. 2022 Mar 18 ; 12 (1) : 4671. [epub] 20220318

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid35304502
Odkazy

PubMed 35304502
PubMed Central PMC8933438
DOI 10.1038/s41598-022-08434-3
PII: 10.1038/s41598-022-08434-3
Knihovny.cz E-zdroje

Eurasian spruce bark beetle (Ips typographus [L.]) causes substantial damage to spruce forests worldwide. Undoubtedly, more aggressive measures are necessary to restrict the enduring loss. Finishing genome sequencing is a landmark achievement for deploying molecular techniques (i.e., RNA interference) to manage this pest. Gene expression studies assist in understanding insect physiology and deployment of molecular approaches for pest management. RT-qPCR is a valuable technique for such studies. However, accuracy and reliability depend on suitable reference genes. With the genome sequence available and the growing requirement of molecular tools for aggressive forest pest management, it is crucial to find suitable reference genes in Ips typographus under different experimental conditions. Hence, we evaluated the stability of twelve candidate reference genes under diverse experimental conditions such as biotic (developmental, sex and tissues) and abiotic factors (i.e., temperature and juvenile hormone treatment) to identify the reference genes. Our results revealed that ribosomal protein 3a (RPS3-a) was the best reference gene across all the experimental conditions, with minor exceptions. However, the stability of the reference gene can differ based on experiments. Nevertheless, present study provides a comprehensive list of reference genes under different experimental conditions for Ips typographus and contributes to "future genomic and functional genomic research".

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Wermelinger B. Ecology and management of the spruce bark beetle Ips typographus: A review of recent research. For. Ecol. Manag. 2004;202(1–3):67–82. doi: 10.1016/j.foreco.2004.07.018. DOI

Sun XL, Yang QY, Sweeney JD, Gao CG. A review: Chemical ecology of Ips typographus (Coleoptera, Scolytidae) J. For. Res. 2006;17:65–70. doi: 10.1007/s11676-006-0016-2. DOI

Raffa KF, Grégoire JC, Lindgren BS. Natural history and ecology of bark beetles. In: Vega FE, Hofstetter RW, editors. Bark Beetles: Biology and Ecology of Native and Invasive Species. Academic Press; 2015. pp. 1–40.

Biedermann P, et al. Bark beetle population dynamics in the anthropocene: Challenges and solutions. Trends Ecol. Evol. 2019;34:914–924. doi: 10.1016/j.tree.2019.06.002. PubMed DOI

Tanin SM, Kandasamy D, Krokene P. Fungal interactions and host tree preferences in the spruce bark beetle Ips typographus. Front. Microbiol. 2021;12:695167. doi: 10.3389/fmicb.2021.695167. PubMed DOI PMC

Sambaraju KR, Côté C. Are climates in Canada and the United States suitable for the European Spruce Bark Beetle, Ips typographus, and Its Fungal Associate, Endoconidiophora polonica? Forests. 2021;12(12):1725. doi: 10.3390/f12121725. DOI

Schelhaas MJ, Nabuurs GJ, Schuck A. Natural disturbances in the European forests in the 19th and 20th centuries. Glob. Change Biol. 2003;9:1620–1633. doi: 10.1046/j.1365-2486.2003.00684.x. DOI

Seidl R, Rammer W, Lexer MJ. Adaptation options to reduce climate change vulnerability of sustainable forest management in the Austrian Alps. Can. J. For. Res. 2011;41:694–706. doi: 10.1139/x10-235. DOI

Bentz BJ, Jönsson AM, Schroeder M, Weed A, Wilcke RAI, Larsson K. Ips typographus and Dendroctonus ponderosae models project thermal suitability for intra- and inter-continental establishment in a changing climate. Front. For. Glob. 2019;2:1.

Knížek, M. Historie a současnost kůrovcových kalamit ve střední Evropě. Zpravodaj ochrany lesa, Škodliví činitelé v lesích Česka, Svazek, 23 (2020). https://www.vulhm.cz/files/uploads/2020/10/ZOL_23_2020.pdf.

Müller J, Bußler H, Goßner M, Rettelbach T, Duelli P. The European spruce bark beetle Ips typographus in a national park: From pest to keystone species. Biodivers. Conserv. 2008;17:2979. doi: 10.1007/s10531-008-9409-1. DOI

Hroššo B, Mezei P, Potterf M, Majdák A, Blaženec M, Korolyova N, Jakuš R. Drivers of Spruce Bark Beetle (Ips typographus) Infestations on downed trees after severe windthrow. Forests. 2020;11:1290. doi: 10.3390/f11121290. DOI

Seidl R, Rammer W, Jäger D, Lexer MJ. Impact of bark beetle (Ips typographus L.) disturbance on timber production and carbon sequestration in different management strategies under climate change. For. Ecol. Manag. 2008;256:209–220. doi: 10.1016/j.foreco.2008.04.002. DOI

Jönsson AM, Appelberg G, Harding S, Bärring L. Spatio-temporal impact of climate change on the activity and voltinism of the spruce bark beetle, Ips typographus. Glob. Change Biol. 2009;15:486–499. doi: 10.1111/j.1365-2486.2008.01742.x. DOI

Ghimire RP, Kivimäenpää M, Blomqvist M, Holopainen T, Lyytikäinen-Saarenmaa P, Holopainen JK. Efect of bark beetle (Ips typographus L.) attack on bark VOC emissions of Norway spruce (Picea abies Karst.) trees. Atmos. Environ. 2016;126:145–152. doi: 10.1016/j.atmosenv.2015.11.049. DOI

Grodzki W, Jakuš J, Lajzová E, Sitková Z, Maczka T, Škvarenina J. Effects of intensive versus no management strategies during an outbreak of the bark beetle Ips typographus (L.) (Col.: Curculionidae, Scolytinae) in the Tatra Mts. in Poland and Slovakia. Ann. For. Sci. 2006;63:55–61. doi: 10.1051/forest:2005097. DOI

Joga MR, Mogilicherla K, Smagghe G, Roy A. RNA interference-based forest protection products (FPPs) against wood-boring coleopterans: Hope or hype? Front. Plant Sci. 2021;12:733608. doi: 10.3389/fpls.2021.733608. PubMed DOI PMC

Bustin SA, et al. The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009;55(4):611–622. doi: 10.1373/clinchem.2008.112797. PubMed DOI

Ginzinger DG. Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Exp. Hematol. 2002;30(6):503–512. doi: 10.1016/s0301-472x(02)00806-8. PubMed DOI

Bustin SA. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems. J. Mol. Endocrinol. 2002;29:23–39. doi: 10.1677/jme.0.0290023. PubMed DOI

Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech. 2004;15:155–166. PubMed PMC

Pinheiro DH, Siegfried BD. Selection of reference genes for normalization of RT-qPCR data in gene expression studies in Anthonomus eugenii Cano (Coleoptera: Curculionidae) Sci. Rep. 2020;10:5070. doi: 10.1038/s41598-020-61739-z. PubMed DOI PMC

Wang Z, Meng Q, Zhu X, Sun S, Liu A, Gao S, Gou Y. Identification and evaluation of reference genes for normalization of gene expression in developmental stages, sexes, and tissues of Diaphania caesalis (Lepidoptera, Pyralidae) J. Insect Sci. 2020;20:1. doi: 10.1093/jisesa/iez130. PubMed DOI PMC

Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Biotechnology (N. Y) 1993;11:1026–1030. doi: 10.1038/nbt0993-1026. PubMed DOI

Vandesompele J, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:1–11. doi: 10.1186/gb-2002-3-7-research0034. PubMed DOI PMC

Bustin SA, Beaulieu JF, Huggett J, et al. MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Mol. Biol. 2010;11:74. doi: 10.1186/1471-2199-11-74. PubMed DOI PMC

Bustin SA, Benes V, Garson JA, et al. Primer sequence disclosure: A clarification of the MIQE guidelines. Clin. Chem. 2011;57(6):919–921. doi: 10.1373/clinchem.2011.162958. PubMed DOI

Yeung N, Botvinick MM, Cohen JD. The neural basis of error detection: Conflict monitoring and the error-related negativity. Psychol. Rev. 2004;111(4):931–959. doi: 10.1037/0033-295x.111.4.939. PubMed DOI

Bustin SA, Benes V, Nolan T, Pfaffl MW. Quantitative real-time RT-PCR—A perspective. J. Mol. Endocrinol. 2005;34:597–601. doi: 10.1677/jme.1.01755. PubMed DOI

Strube C, Buschbaum S, Wolken S, Schnieder T. Evaluation of reference genes for quantitative real-time PCR to investigate protein disulfide is omerase transcription pattern in the bovine lungworm Dictyocaulus viviparus. Gene. 2008;425:36–43. doi: 10.1016/j.gene.2008.08.001. PubMed DOI

Gao P, Wang J, Wen J. Selection of reference genes for tissue/organ samples of adults of Eucryptorrhynchus scrobiculatus. PLoS ONE. 2020;15(2):e0228308. doi: 10.1371/journal.pone.0228308. PubMed DOI PMC

Ponton F, Chapuis MP, Pernice M, Sword GA, Simpson SJ. Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster. J. Insect Physiol. 2011;57(6):840–850. doi: 10.1016/j.jinsphys.2011.03.014. PubMed DOI

Yang XW, Pan HP, Yuan L, Zhou X. Reference gene selection for RT-qPCR analysis in Harmonia axyridis, a global invasive lady beetle. Sci. Rep. 2018;8:2689. doi: 10.1038/s41598-018-20612-w. PubMed DOI PMC

Koramutla MK, Aminedi R, Bhattacharya R. Comprehensive evaluation of candidate reference genes for qRT-PCR studies of gene expression in mustard aphid, Lipaphis erysimi (Kalt) Sci. Rep. 2016;6:25883. doi: 10.1038/srep25883. PubMed DOI PMC

Arya SK, Jain G, Upadhyay SK, Sarita SH, Dixit S, Verma PC. Reference genes validation in Phenacoccus solenopsis under various biotic and abiotic stress conditions. Sci. Rep. 2017;7:13520. doi: 10.1038/s41598-017-13925-9. PubMed DOI PMC

García-Reina A, Rodríguez-García MJ, Galián J. Validation of reference genes for quantitative real-time PCR in tiger beetles across sexes, body parts, sexual maturity and immune challenge. Sci. Rep. 2018;8:10743. doi: 10.1038/s41598-018-28978-7. PubMed DOI PMC

Shakeel M, Rodriguez A, Tahir UB, Jin F. Gene expression studies of reference genes for quantitative real-time PCR: An overview in insects. Biotechnol. Lett. 2018;40:227–236. doi: 10.1007/s10529-017-2465-4. PubMed DOI

Lu 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. Front. Physiol. 2018;9:1560. doi: 10.3389/fphys.2018.01560. PubMed DOI PMC

Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pairwise correlations. Biotechnol. Lett. 2004;26:509–515. doi: 10.1023/b:bile.0000019559.84305.47. PubMed DOI

Qu C, Wang R, Che W, Zhu X, Li F, Luo C. Selection and evaluation of reference genes for expression analysis using quantitative real-time PCR in the Asian Ladybird Harmonia axyridis (Coleoptera: Coccinellidae) PLoS ONE. 2018;13(6):e0192521. doi: 10.1371/journal.pone.0192521. PubMed DOI PMC

Basu S, et al. Evaluation of reference genes for real-time quantitative PCR analysis in southern corn rootworm, Diabrotica undecimpunctata howardi (Barber) Sci. Rep. 2019;9:10703. doi: 10.1038/s41598-019-47020-y. PubMed DOI PMC

Xie J, Liu T, Khashaveh A, Yi C, Liu X, Zhang Y. Identification and evaluation of suitable reference genes for RT-qPCR analysis in Hippodamia variegata (Coleoptera: Coccinellidae) under different biotic and abiotic conditions. Front. Physiol. 2021;12:669510. doi: 10.3389/fphys.2021.669510. PubMed DOI PMC

Sellamuthu G, et al. Reference gene selection for normalizing gene expression in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae) under different experimental conditions. Front. Physiol. 2021 doi: 10.3389/fphys.2021.752768. PubMed DOI PMC

Powell D, et al. A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest. Commun. Biol. 2021;4:1059. doi: 10.1038/s42003-021-02602-3. PubMed DOI PMC

Remeš J, Podrázský V. Fertilization of spruce monocultures on the School Training Forest territory in Kostelec nad Černými lesy. J. For. Sci. 2006;52(1):73–78. doi: 10.17221/10163-JFS. DOI

Hlásny T, Zimová S, Merganičová K, Štěpánek P, Modlinger R, Turčáni M. Devastating outbreak of bark beetles in the Czech Republic: Drivers, impacts, and management implications. For. Ecol. Manag. 2021;490:119075. doi: 10.1016/j.foreco.2021.119075. DOI

Hall GM, et al. Midgut tissue of male pine engraver, Ips pini, synthesizes monoterpenoid pheromone component ipsdienol de novo. Naturwissenschaften. 2002;89:79–83. doi: 10.1007/s00114-001-0290-y. PubMed DOI

Sun Y, Fu F, Kang X, Liu B, Ning H, Chen H. Function of mevalonate pathway genes in the synthesis of frontalin in Chinese white pine beetle, Dendroctonus armandi (curculionidae: Scolytinae) Arch. Insect Biochem. Physiol. 2021;107(4):1–13. doi: 10.1002/arch.21828. PubMed DOI

Andersen CL, Jensen JL, Orntoft TF. 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. 2004;64:5245–5250. doi: 10.1158/0008-5472.can-04-0496. PubMed DOI

Silver N, Best S, Jiang J, Thein SL. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol. Biol. 2006;6:33. doi: 10.1186/1471-2199-7-33. PubMed DOI PMC

Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001;25:402–408. doi: 10.1006/meth.2001.1262. PubMed DOI

Tellin O, et al. Housekeeping genes as internal standards: Use and limits. J. Biotechnol. 1999;75:291–295. doi: 10.1016/S0168-1656(99)00163-7. PubMed DOI

Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6:279–284. doi: 10.1038/sj.gene.6364190. PubMed DOI

Ryan MG, Sapes G, Sala A, Hood SM. Tree physiology and bark beetles. New Phytol. 2015;205:955–957. doi: 10.1111/nph.13256. PubMed DOI

Kausrud K, Økland B, Skarpaas O, Grégoire JC, Erbilgin N, Stenseth NC. Population dynamics in changing environments: The case of an eruptive forest pest species. Biol. Rev. 2012;87:34–51. doi: 10.1111/j.1469185X.2011.00183.x. PubMed DOI

Fettig C. J., et al. Bark Beetle Management, Ecology, and Climate Change (ed. Gandhi K. J. K & Hofstetter, R. W). 345–394, Academic Press (2021)

Zhou X, Liao WJ, Liao JM, Liao P, Lu H. Ribosomal proteins: Functions beyond the ribosome. J. Mol. Cell Biol. 2015;7(2):92–104. doi: 10.1093/jmcb/mjv014. PubMed DOI PMC

Saha A, et al. Genome-wide identification and comprehensive expression profiling of ribosomal protein small subunit (RPS) genes and their comparative analysis with the large subunit (RPL) genes in rice. Front. Plant Sci. 2017;8:1553. doi: 10.3389/fpls.2017.01553. PubMed DOI PMC

Petibon C, Malik GM, Catala M, Abou ES. Regulation of ribosomal protein genes: An ordered anarchy. Wiley Interdiscip. Rev. RNA. 2021;12(3):1632. doi: 10.1002/wrna.1632. PubMed DOI PMC

Lee CH, et al. A regulatory response to ribosomal protein mutations controls translation, growth, and cell competition. Develop. Cell. 2018;46(4):456–469. doi: 10.1016/j.devcel.2018.07.003. PubMed DOI PMC

Yan X, Zhang Y, Xu K, Wang Y, Yang W. Selection and validation of reference genes for gene expression analysis in Tuta absoluta Meyrick (Lepidoptera: Gelechiidae) Insects. 2021;12:589. doi: 10.3390/insects12070589. PubMed DOI PMC

Lu Y, et al. Identification and validation of reference genes for gene expression analysis using quantitative PCR in Spodoptera litura (Lepidoptera: Noctuidae) PLoS ONE. 2013;8:e68059. doi: 10.1371/journal.pone.0068059. PubMed DOI PMC

Li HB, Dai CG, Zhang CR, He YF, Ran HY, Chen SH. Screening potential reference genes for quantitative real-time PCR analysis in the oriental armyworm, Mythimna separata. PLoS ONE. 2018;13(4):e0195096. doi: 10.1371/journal.pone.0195096. PubMed DOI PMC

Zhou L, Meng JY, Ruan HY, Yang CL, Zhang CY. Expression stability of candidate RT-qPCR housekeeping genes in Spodoptera frugiperda (Lepidoptera: Noctuidae) Arch. Insect Biochem. Physiol. 2021;108:e21831. doi: 10.1002/arch.21831. PubMed DOI

Bai Y, et al. Selection of reference genes for normalization of gene expression in Thermobia domestica (Insecta: Zygentoma: Lepismatidae) Genes. 2021;12(1):21. doi: 10.3390/genes12010021. PubMed DOI PMC

Li M, et al. Selection and validation of reference genes for qRT-PCR analysis of Rhopalosiphum padi (Hemiptera: Aphididae) Front. Physiol. 2021;12:663338. doi: 10.3389/fphys.2021.663338. PubMed DOI PMC

Su RR, Huang ZY, Qin CW, Zheng XL, Lu W, Wang XY. Evaluation of reference genes in Glenea cantor (Fabricius) by using qRT-PCR. Genes. 2021;12:1984. doi: 10.3390/genes12121984. PubMed DOI PMC

Wang Y, Wang ZK, Huang Y, Liao YF, Yin YP. Identification of suitable reference genes for gene expression studies by qRT-PCR in the blister beetle Mylabris cichorii. J. Insect Sci. 2014;14:94. doi: 10.1093/jis/14.1.94. PubMed DOI PMC

Rodrigues TB, Dhandapani RK, Duan JJ, Palli SR. RNA interference in the Asian Longhorned Beetle: Identification of key RNAi genes and reference genes for RT-qPCR. Sci. Rep. 2017;7(1):8913. doi: 10.1038/s41598-017-08813-1. PubMed DOI PMC

Liu G, Qiu X, Cao L, Zhang Y, Zhan Z, Han R. Evaluation of reference genes for reverse transcription quantitative PCR studies of physiological responses in the ghost moth, Thitarodes armoricanus (Lepidoptera, Hepialidae) PLoS ONE. 2016;11(7):e0159060. doi: 10.1371/journal.pone.0159060. PubMed DOI PMC

Khan MM, Guo CF, Peng J, Fan ZN, Hafeez M, Ali D, Wang K, Almarzoug MHA, Qiu BL. Screening and validation of reference genes using in RT-qPCR for gene expression studies in Paederus fuscipes, a medically and agriculturally important insect. J. King Saud. Univ. Sci. 2022;1:101654. doi: 10.1016/j.jksus.2021.101654. DOI

Tao J, et al. Systematic identification of housekeeping genes possibly used as references in Caenorhabditis elegans by large-scale data integration. Cells. 2020;9(3):786. doi: 10.3390/cells9030786. PubMed DOI PMC

Fu W, et al. Exploring valid reference genes for quantitative real-time PCR analysis in Plutella xylostella (Lepidoptera: Plutellidae) Int. J. Biol. Sci. 2013;9(8):792–802. doi: 10.7150/ijbs.5862. PubMed DOI PMC

Negrutskii BS, El'skaya AV. Eukaryotic translation elongation factor 1 alpha: Structure, expression, functions, and possible role in aminoacyl-tRNA channeling. Prog. Nucleic Acid Res. Mol. Biol. 1998;60:47–78. doi: 10.1016/s0079-6603(08)60889-2. PubMed DOI

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. 2012;12:1–17. doi: 10.1673/031.012.6001. PubMed DOI PMC

Rajarapu SP, Mamidala P, Mittapalli O. Validation of reference genes for gene expression studies in the emerald ash borer (Agrilus planipennis) Insect Sci. 2012;19:41–46. doi: 10.1111/j.1744-7917.2011.01447.x. DOI

An XK, Hou ML, Liu YD. Reference gene selection and evaluation for gene expression studies using qRT-PCR in the white-backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae) J. Econ. Entomol. 2016;109:879. doi: 10.1093/jee/tov333. PubMed DOI

Li K, Xu N, Yang YJ, Zhang JH, Yin H. Identification and validation of reference genes for RT-qPCR normalization in Mythimna separata (Lepidoptera: Noctuidae) Biomed. Res. Int. 2018 doi: 10.1155/2018/1828253. PubMed DOI PMC

Zhang H, Zhao M, Liu Y, Zhou Z, Guo J. Identification of cytochrome P450 monooxygenase genes and their expression in response to high temperature in the alligator weed flea beetle Agasicles hygrophila (Coleoptera: Chrysomelidae) Sci. Rep. 2018;8:17847. doi: 10.1038/s41598-018-35993-1. PubMed DOI PMC

Peng L, et al. Functional study of cytochrome P450 enzymes from the brown planthopper (Nilaparvata lugens Stål) to analyze Its adaptation to BPH-resistant rice. Front. Physiol. 2017;8:972. doi: 10.3389/fphys.2017.00972. PubMed DOI PMC

Chung H, Sztal T, Pasricha S, Sridhar M, Batterham P, Daborn PJ. Characterization of Drosophila melanogaster cytochrome P450 genes. Proc. Natl. Acad. Sci. U. S. A. 2009;106:5731–5736. doi: 10.1073/pnas.0812141106. PubMed DOI PMC

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