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de Sousa FCB, do Nascimento CS, Macário MDS, Araújo RDS, Barbosa LT, Bayão GFV, Sousa KRS. Selection of reference genes for quantitative real-time PCR normalization in European quail tissues. Mol Biol Rep 2021; 48:67-76. [PMID: 33454906 DOI: 10.1007/s11033-020-06134-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Coturniculture has been standing out as an industrial poultry activity in several countries around the world because of the several adaptive advantages of quails. Research that considers the analysis of gene expression can enhance this activity. This study aimed to analyze the stability of reference genes (RGs) in different tissues of quails (both males and females) for the recommendation of use in gene expression studies by the quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The expression stability of ten RGs (ACTA1, ACTB, B2M, GAPDH, HMBS, SDHA, HPRT1, MRPS27, MRPS30, and RPL5) was analyzed in four tissues (breast muscle, abdominal fat, liver, and intestine), and assessed using the statistical tools geNorm, NormFinder, comparative ΔCq method, and BestKeeper. The HPRT1 gene was the most stable in all quail tissues tested, followed by MRPS27 and MRPS30 in breast muscle, B2M and RPL5 in abdominal fat, HMBS and B2M in the liver, and RPL5 and HMBS in the intestine. These results may help studies using RT-qPCR assays to assess quail tissues from both sexes because they provide data on the most stable genes, which should be tested as candidate RGs for other experimental conditions.
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Affiliation(s)
| | | | - Maíse Dos Santos Macário
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, SE, 49100-000, Brazil
| | | | - Leandro Teixeira Barbosa
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, SE, 49100-000, Brazil
| | - Geraldo Fábio Viana Bayão
- Department of Animal Science, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, São Luís, MA, 65095-460, Brazil
| | - Katiene Régia Silva Sousa
- Department of Oceanography and Limnology, Universidade Federal do Maranhão, São Luís, MA, 65080-805, Brazil
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Selection and Validation of Reference Genes for Quantitative Real-Time PCR in White Clover ( Trifolium repens L.) Involved in Five Abiotic Stresses. PLANTS 2020; 9:plants9080996. [PMID: 32764378 PMCID: PMC7463471 DOI: 10.3390/plants9080996] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Accepted: 08/02/2020] [Indexed: 01/28/2023]
Abstract
White clover (Trifolium repens L.) is a widely cultivated cool-season perennial forage legume in temperate grassland systems. Many studies have analyzed the gene expression in this grass species using quantitative real-time reverse transcription PCR (qRT-PCR). The selection of stable reference genes for qRT-PCR is crucial. However, there was no detailed study on reference genes in different tissues of white clover under various abiotic stress conditions. Herein, 14 candidate reference genes (ACT7, ACT101, TUA1109, TUB, CYP, 60SrRNA, UBQ, E3, GAPDH1, GAPDH2, PP2A, BAM3, SAMDC, and ABC) were selected and analyzed by four programs (GeNorm, NormFinder, BestKeeper, and RefFinder). Samples were taken from two tissues (leaves and roots) under five different abiotic stresses (drought, salt, heat, cold, and heavy metal stress). Our results showed that 60SrRNA and ACT101 were the two top-ranked genes for all samples. Under various experimental conditions, the most stable gene was different; however, SAMDC, UBQ, 60SrRNA, and ACT101 were always top ranked. The most suitable reference genes should be selected according to different plant tissues and growth conditions. Validation of these reference genes by expression analysis of Cyt-Cu/Zn SOD and CAT confirmed their reliability. Our study will benefit the subsequent research of gene function in this species.
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Foquet B, Song H. There is no magic bullet: the importance of testing reference gene stability in RT-qPCR experiments across multiple closely related species. PeerJ 2020; 8:e9618. [PMID: 32832268 PMCID: PMC7409783 DOI: 10.7717/peerj.9618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/06/2020] [Indexed: 11/20/2022] Open
Abstract
Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR) is the current gold standard tool for the study of gene expression. This technique is highly dependent on the validation of reference genes, which exhibit stable expression levels among experimental conditions. Often, reference genes are assumed to be stable a priori without a rigorous test of gene stability. However, such an oversight can easily lead to misinterpreting expression levels of target genes if the references genes are in fact not stable across experimental conditions. Even though most gene expression studies focus on just one species, comparative studies of gene expression among closely related species can be very informative from an evolutionary perspective. In our study, we have attempted to find stable reference genes for four closely related species of grasshoppers (Orthoptera: Acrididae) that together exhibit a spectrum of density-dependent phenotypic plasticity. Gene stability was assessed for eight reference genes in two tissues, two experimental conditions and all four species. We observed clear differences in the stability ranking of these reference genes, both between tissues and between species. Additionally, the choice of reference genes clearly influenced the results of a gene expression experiment. We offer suggestions for the use of reference genes in further studies using these four species, which should be taken as a cautionary tale for future studies involving RT-qPCR in a comparative framework.
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Affiliation(s)
- Bert Foquet
- Department of Entomology, Texas A&M University, College Station, TX, United States of America
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, United States of America
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Haeberlein S, Angrisano A, Quack T, Lu Z, Kellershohn J, Blohm A, Grevelding CG, Hahnel SR. Identification of a new panel of reference genes to study pairing-dependent gene expression in Schistosoma mansoni. Int J Parasitol 2019; 49:615-624. [PMID: 31136746 DOI: 10.1016/j.ijpara.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 12/18/2022]
Abstract
Facilitated by the Schistosoma mansoni genome project, multiple transcriptomic studies were performed over the last decade to elucidate gene expression patterns among different developmental stages of the complex schistosome life cycle. While these analyses enable the identification of candidate genes with key functions in schistosome biology, a diverse molecular tool set is needed that allows comprehensive functional characterization at the single gene level. This includes the availability of reliable reference genes to confirm changes in the transcription of genes of interest over different biological samples and experimental conditions. In particular, the investigation of one key aspect of schistosome biology, the pairing-dependent gene expression in females and males, requires knowledge on reference genes that are expressed independently of both pairing and of in vitro culture effects. Therefore, the present study focused on the identification of quantitative reverse transcription (qRT)-PCR reference genes suitable for the investigation of pairing-dependent gene expression in the S. mansoni male. The "pipeline" we present here is based on qRT-PCR analyses of high biological replication combined with three different statistical analysis tools, BestKeeper, geNorm, and NormFinder. Our approach resulted in a statistically robust ranking of 15 selected reference genes with respect to their transcription stability between pairing-unexperienced and -experienced males. We further tested the top seven candidate genes for their transcription stability during invitro culture of adult S. mansoni. Of these, the two most suitable reference genes were used to investigate the influence of the pairing contact on the transcription of genes of interest, comprising a tyrosine decarboxylase gene Smtdc1, an ebony ortholog Smebony, and the follistatin ortholog Smfst in S. mansoni males. Performing pairing, separation and re-pairing experiments with adult S. mansoni in vitro, our results indicate for the first time that pairing can act as a molecular on/off-switch of specific genes to strictly control their expression in schistosome males.
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Affiliation(s)
- Simone Haeberlein
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Thomas Quack
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Josina Kellershohn
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Ariane Blohm
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Steffen R Hahnel
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany.
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Yokoyama T, Omotehara T, Hirano T, Kubota N, Yanai S, Hasegawa C, Takada T, Mantani Y, Hoshi N. Identification of reference genes for quantitative PCR analyses in developing mouse gonads. J Vet Med Sci 2018; 80:1534-1539. [PMID: 30175754 PMCID: PMC6207531 DOI: 10.1292/jvms.18-0417] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Stable reference genes are important for gene expression analyses such as quantitative
PCR. The stability of 15 candidate reference genes that can be used to developing mouse
gonads was thoroughly verified using combinations of multiple algorithms. The expression
of these genes fluctuated greatly depending on the analysis period and/or gender.
Peptidylprolyl isomerase A (Ppia) and polymerase (RNA) II (DNA directed)
polypeptide A (Polr2a) were the reference genes that were used stably for
a wide analysis period in developing mouse gonads. Furthermore, the stable reference genes
corresponding to the analysis period and/or gender were ranked. These results are useful
for the selection of the optimal reference gene required for high-precision
measurements.
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Affiliation(s)
- Toshifumi Yokoyama
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Takuya Omotehara
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.,Department of Anatomy, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku, Tokyo 160-8402, Japan
| | - Tetsushi Hirano
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.,Division of Drug and Structural Research, Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Naoto Kubota
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Shogo Yanai
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Chinatsu Hasegawa
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Tadashi Takada
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yohei Mantani
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Nobuhiko Hoshi
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
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Weyrich A, Benz S, Karl S, Jeschek M, Jewgenow K, Fickel J. Paternal heat exposure causes DNA methylation and gene expression changes of Stat3 in Wild guinea pig sons. Ecol Evol 2016; 6:2657-66. [PMID: 27066228 PMCID: PMC4769883 DOI: 10.1002/ece3.1993] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/18/2015] [Accepted: 01/18/2016] [Indexed: 12/31/2022] Open
Abstract
Epigenetic mechanisms convey environmental information through generations and can regulate gene expression. Epigenetic studies in wild mammals are rare, but enable understanding adaptation processes as they may occur in nature. In most wild mammal species, males are the dispersing sex and thus often have to cope with differing habitats and thermal changes more rapidly than the often philopatric females. As temperature is a major environmental selection factor, we investigated whether genetically heterogeneous Wild guinea pig (Cavia aperea) males adapt epigenetically to an increase in temperature, whether that response will be transmitted to the next generation(s), and whether it regulates mRNA expression. Five (F0) adult male guinea pigs were exposed to an increased ambient temperature for 2 months, corresponding to the duration of the species' spermatogenesis. To study the effect of heat, we focused on the main thermoregulatory organ, the liver. We analyzed CpG‐methylation changes of male offspring (F1) sired before and after the fathers' heat treatment (as has recently been described in Weyrich et al. [Mol. Ecol., 2015]). Transcription analysis was performed for the three genes with the highest number of differentially methylated changes detected: the thermoregulation gene Signal Transducer and Activator of Transcription 3 (Stat3), the proteolytic peptidase gene Cathepsin Z (Ctsz), and Sirtuin 6 (Sirt6) with function in epigenetic regulation. Stat3 gene expression was significantly reduced (P < 0.05), which indicated a close link between CpG‐methylation and expression levels for this gene. The two other genes did not show gene expression changes. Our results indicate the presence of a paternal transgenerational epigenetic effect. Quick adaptation to climatic changes may become increasingly relevant for the survival of wildlife species as global temperatures are rising.
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Affiliation(s)
- Alexandra Weyrich
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Stephanie Benz
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Stephan Karl
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Marie Jeschek
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Alfred-Kowalke-Str. 17D-10315 Berlin Germany; Berlin Center for Genomics in Biodiversity Research Koenigin-Luise-Str. 6-814195 Berlin Germany
| | - Katarina Jewgenow
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Joerns Fickel
- Leibniz-Institute for Zoo and Wildlife Research (IZW)Alfred-Kowalke-Str. 17D-10315 Berlin Germany; Potsdam University Karl-Liebknecht-Str. 22-2414476 Potsdam Germany
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Reference genes in real-time PCR. J Appl Genet 2014; 54:391-406. [PMID: 24078518 PMCID: PMC3825189 DOI: 10.1007/s13353-013-0173-x] [Citation(s) in RCA: 597] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 10/31/2022]
Abstract
This paper aims to discuss various aspects of the use of reference genes in qPCR technique used in the thousands of present studies. Most frequently, these are housekeeping genes and they must meet several criteria so that they can lay claim to the name. Lots of papers report that in different conditions, for different organisms and even tissues the basic assumption—the constant level of the expression is not maintained for many genes that seem to be perfect candidates. Moreover, their transcription can not be affected by experimental factors. Sounds simple and clear but a great number of designed protocols and lack of consistency among them brings confusion on how to perform experiment properly. Since during selection of the most stable normalizing gene we can not use any reference gene, different ways and algorithms for their selection were developed. Such methods, including examples of best normalizing genes in some specific cases and possible mistakes are presented based on available sources. Numerous examples of reference genes applications, which are usually in too few numbers in relevant articles not allowing to make a solid fundament for a reader, will be shown along with instructive compilations to make an evidence for presented statements and an arrangement of future qPCR experiments. To include all the pitfalls and problems associated with the normalization methods there is no way not to begin from sample preparation and its storage going through candidate gene selection, primer design and statistical analysis. This is important because numerous short reviews available cover the topic only in lesser extent at the same time giving the reader false conviction of complete topic recognition.
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Zhong M, Wang X, Wen J, Cai J, Wu C, Aly SM. Selection of reference genes for quantitative gene expression studies in the house fly (Musca domestica L.) using reverse transcription quantitative real-time PCR. Acta Biochim Biophys Sin (Shanghai) 2013; 45:1069-73. [PMID: 24113091 DOI: 10.1093/abbs/gmt111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ming Zhong
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
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Sommer S, Courtiol A, Mazzoni CJ. MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. BMC Genomics 2013; 14:542. [PMID: 23937623 PMCID: PMC3750822 DOI: 10.1186/1471-2164-14-542] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 07/30/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required. RESULTS We developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future. CONCLUSIONS Combining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent applications.
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Affiliation(s)
- Simone Sommer
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
| | - Alexandre Courtiol
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
| | - Camila J Mazzoni
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Koenigin-Luise-Straße 6-8, D-14195 Berlin, Germany
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Li XS, Yang HL, Zhang DY, Zhang YM, Wood AJ. Reference gene selection in the desert plant Eremosparton songoricum. Int J Mol Sci 2012; 13:6944-6963. [PMID: 22837673 PMCID: PMC3397505 DOI: 10.3390/ijms13066944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/03/2012] [Accepted: 05/30/2012] [Indexed: 11/30/2022] Open
Abstract
Eremosparton songoricum (Litv.) Vass. (E. songoricum) is a rare and extremely drought-tolerant desert plant that holds promise as a model organism for the identification of genes associated with water deficit stress. Here, we cloned and evaluated the expression of eight candidate reference genes using quantitative real-time reverse transcriptase polymerase chain reactions. The expression of these candidate reference genes was analyzed in a diverse set of 20 samples including various E. songoricum plant tissues exposed to multiple environmental stresses. GeNorm analysis indicated that expression stability varied between the reference genes in the different experimental conditions, but the two most stable reference genes were sufficient for normalization in most conditions. EsEF and Esα-TUB were sufficient for various stress conditions, EsEF and EsACT were suitable for samples of differing germination stages, and EsGAPDHand EsUBQ were most stable across multiple adult tissue samples. The Es18S gene was unsuitable as a reference gene in our analysis. In addition, the expression level of the drought-stress related transcription factor EsDREB2 verified the utility of E. songoricum reference genes and indicated that no single gene was adequate for normalization on its own. This is the first systematic report on the selection of reference genes in E. songoricum, and these data will facilitate future work on gene expression in this species.
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Affiliation(s)
- Xiao-Shuang Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; E-Mails: (X.-S.L.); (H.-L.Y.); (Y.-M.Z.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Lan Yang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; E-Mails: (X.-S.L.); (H.-L.Y.); (Y.-M.Z.)
| | - Dao-Yuan Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; E-Mails: (X.-S.L.); (H.-L.Y.); (Y.-M.Z.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-991-7823109; Fax: +86-991-7823109
| | - Yuan-Ming Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; E-Mails: (X.-S.L.); (H.-L.Y.); (Y.-M.Z.)
| | - Andrew J. Wood
- Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901, USA; E-Mail:
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Maroniche GA, Sagadín M, Mongelli VC, Truol GA, del Vas M. Reference gene selection for gene expression studies using RT-qPCR in virus-infected planthoppers. Virol J 2011; 8:308. [PMID: 21679431 PMCID: PMC3142240 DOI: 10.1186/1743-422x-8-308] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/16/2011] [Indexed: 12/28/2022] Open
Abstract
Background Planthoppers not only severely affect crops by causing mechanical damage when feeding but are also vectors of several plant virus species. The analysis of gene expression in persistently infected planthoppers might unveil the molecular basis of viral transmission. Quantitative real-time RT-PCR (RT-qPCR) is currently the most accurate and sensitive method used for quantitative gene expression analysis. In order to normalize the resulting quantitative data, reference genes with constant expression during the experimental procedures are needed. Results Partial sequences of the commonly used reference genes actin (ACT), α1-tubulin (TUB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1A), ribosomal protein S18 (RPS18) and polyubiquitin C (UBI) from Delphacodes kuscheli, a planthopper capable of persistently transmitting the plant fijivirus Mal de Río Cuarto virus (MRCV), were isolated for the first time. Specific RT-qPCR primers were designed and the expression stability of these genes was assayed in MRCV-infective and naïve planthoppers using geNorm, Normfinder and BestKeeper tools. The overall analysis showed that UBI, followed by 18S and ACT, are the most suitable genes as internal controls for quantitative gene expression studies in MRCV-infective planthoppers, while TUB and EF1A are the most variable ones. Moreover, EF1A was upregulated by MRCV infection. Conclusions A RT-qPCR platform for gene expression analysis in the MRCV-infected planthopper vector Delphacodes kuscheli was developed. Our work is the first report on reference gene selection in virus-infected insects, and might serve as a precedent for future gene expression studies on MRCV and other virus-planthopper pathosystems.
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Affiliation(s)
- Guillermo A Maroniche
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Las Cabañas y Los Reseros s/n, Hurlingham CP 1686, Buenos Aires, Argentina
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Castro-Prieto A, Wachter B, Sommer S. Cheetah paradigm revisited: MHC diversity in the world's largest free-ranging population. Mol Biol Evol 2011; 28:1455-68. [PMID: 21183613 PMCID: PMC7187558 DOI: 10.1093/molbev/msq330] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For more than two decades, the cheetah (Acinonyx jubatus) has been considered a paradigm of disease vulnerability associated with low genetic diversity, particularly at the immune genes of the major histocompatibility complex (MHC). Cheetahs have been used as a classic example in numerous conservation genetics textbooks as well as in many related scientific publications. However, earlier studies used methods with low resolution to quantify MHC diversity and/or small sample sizes. Furthermore, high disease susceptibility was reported only for captive cheetahs, whereas free-ranging cheetahs show no signs of infectious diseases and a good general health status. We examined whether the diversity at MHC class I and class II-DRB loci in 149 Namibian cheetahs was higher than previously reported using single-strand conformation polymorphism analysis, cloning, and sequencing. MHC genes were examined at the genomic and transcriptomic levels. We detected ten MHC class I and four class II-DRB alleles, of which nine MHC class I and all class II-DRB alleles were expressed. Phylogenetic analyses and individual genotypes suggested that the alleles belong to four MHC class I and three class II-DRB putative loci. Evidence of positive selection was detected in both MHC loci. Our study indicated that the low number of MHC class I alleles previously observed in cheetahs was due to a smaller sample size examined. On the other hand, the low number of MHC class II-DRB alleles previously observed in cheetahs was further confirmed. Compared with other mammalian species including felids, cheetahs showed low levels of MHC diversity, but this does not seem to influence the immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease vulnerability.
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Affiliation(s)
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simone Sommer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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Guivier E, Galan M, Salvador AR, Xuéreb A, Chaval Y, Olsson GE, Essbauer S, Henttonen H, Voutilainen L, Cosson JF, Charbonnel N. Tnf-α expression and promoter sequences reflect the balance of tolerance/resistance to Puumala hantavirus infection in European bank vole populations. INFECTION GENETICS AND EVOLUTION 2010; 10:1208-17. [PMID: 20691810 DOI: 10.1016/j.meegid.2010.07.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/12/2010] [Accepted: 07/29/2010] [Indexed: 01/17/2023]
Abstract
The tumor necrosis factor-alpha (TNF-α) influences the ability to limit parasite infection but its over-production might result in inflammatory disorders. The level of Tnf-α gene expression could thus mediate a balance of tolerance/resistance to infections. This study focused on Puumala hantavirus (PUUV) infection in its rodent host, the bank vole (Myodes glareolus). In humans, PUUV is responsible of a mild form of hemorrhagic fever with renal syndrome, nephropathia epidemica (NE). The severity of NE is associated with an over-production of TNF-α. By contrast, PUUV infection in bank vole is chronic and asymptomatic. It is likely that different coevolutionary histories between PUUV and its hosts could lead to different balances of resistance/tolerance to PUUV infection, at least partly mediated by variable production levels of TNF-α. We investigated the hypothesis that bank voles from PUUV endemic areas should exhibit higher levels of tolerance, i.e. lower levels of TNF-α production, than bank voles from areas where PUUV prevalence is low. For this purpose, we analysed variations of Tnf-α gene expression and promoter sequences among European populations of bank voles. Our results revealed an absence of up-regulation of Tnf-α gene expression in PUUV infected bank voles and significant differences in Tnf-α gene expression level with regard to PUUV endemicity. These results corroborated the hypothesis of different balances of tolerance/resistance to PUUV. Two single-nucleotide polymorphism genotypes within the Tnf-α promoter (-302 GG/GG and -296 A/A) were associated with higher Tnf-α gene expression and were more frequent in non-endemic areas. This study emphasized the potential influence of selection acting on TNF-α production and mediating a tolerance/resistance balance to PUUV in bank voles. Further investigations, including the role of phenotypic plasticity and parasite communities on Tnf-α expression levels, should provide important keys to understand the prevalence of PUUV over Europe.
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Affiliation(s)
- Emmanuel Guivier
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, France.
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