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Daude MM, Ságio SA, Rodrigues JN, Lima NMP, Lima AA, Sarmento MI, Sarmento RA, Barreto HG. Reference genes for Eucalyptus spp. under Beauveria bassiana inoculation and subsequently infestation by the galling wasp Leptocybe invasa. Sci Rep 2024; 14:2556. [PMID: 38297150 PMCID: PMC10830493 DOI: 10.1038/s41598-024-52948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
Relative gene expression analysis through RT-qPCR is an important molecular technique that helps understanding different molecular mechanisms, such as the plant defense response to insect pests. However, the use of RT-qPCR for gene expression analysis can be affected by factors that directly affect the reliability of the results. Among these factors, the appropriate choice of reference genes is crucial and can strongly impact RT-qPCR relative gene expression analyses, highlighting the importance in correctly choosing the most suitable genes for the success of the analysis. Thus, this study aimed to select and validate reference genes for relative gene expression studies through RT-qPCR in hybrids of Eucalyptus tereticornis × Eucalyptus camaldulensis (drought tolerant and susceptible to Leptocybe invasa) under conditions of inoculation by the Beauveria bassiana fungus and subsequent infestation by L. invasa. The expression level and stability of eleven candidate genes were evaluated. Stability was analyzed using the RefFinder tool, which integrates the geNorm, NormFinder, BestKeeper, and Delta-Ct algorithms. The selected reference genes were validated through the expression analysis of the transcriptional factor EcDREB2 (dehydration-responsive element-binding protein 2). For all treatments evaluated, EcPTB, EcPP2A-1, and EcEUC12 were the best reference genes. The triplets EcPTB/EcEUC12/EcUBP6, EcPP2A-1/EcEUC12/EcPTB, EcIDH/EcSAND/Ecα-TUB, EcPP2A-1/Ecα-TUB/EcPTB, and EcPP2A-1/EcUPL7/EcSAND were the best reference genes for the control plants, mother plants, plants inoculated with B. bassiana, plants infested with L. invasa, and plants inoculated with B. bassiana and subsequently infested with L. invasa, respectively. The best determined reference genes were used to normalize the RT-qPCR expression data for each experimental condition evaluated. The results emphasize the importance of this type of study to ensure the reliability of relative gene expression analyses. Furthermore, the findings of this study can be used as a basis for future research, comprising gene expression analysis of different eucalyptus metabolic pathways.
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Affiliation(s)
- Matheus Martins Daude
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil
| | - Solange Aparecida Ságio
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Digital Agroenergy, Federal University of Tocantins, Palmas, TO, Brazil
| | - Jovielly Neves Rodrigues
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | | | - André Almeida Lima
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
| | - Maíra Ignacio Sarmento
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | - Renato Almeida Sarmento
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil.
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil.
- Postgraduate Program in Digital Agroenergy, Federal University of Tocantins, Palmas, TO, Brazil.
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Daúde MM, Teixeira RC, Cardon CH, de Araujo Santos GC, de Almeida AF, Chalfun-Junior A, Barreto HG. Selection and validation of reference genes for RT-qPCR gene expression studies in Candida viswanathii cultivated under different grown conditions. J Microbiol Methods 2023:106777. [PMID: 37419333 DOI: 10.1016/j.mimet.2023.106777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
The properties presented by Candida viswanathii's lipases turn this specie into a promising producer of potentially applicable lipases in several industrial sectors, such as: food, textiles, in the oleochemical and paper industries, and also in different pharmaceutical applications. However, studies for elucidating growth and developmental processes at the molecular level in this species are still incipient. Performing such kinds of studies often rely on the use of the RT-qPCR, which is a highly sensitivity technique, but whose parameters must be carefully planned for achieving reliable data. Among the crucial parameters required for achieving reliable results through this technique, the use of appropriated and validated reference genes is one the most important, constituting a bottleneck, mainly in species where molecular studies are scarce. Thus, the aim of this study was to determine the best reference genes for RT-qPCR gene expression studies in C. viswanathii grown in culture media containing four different carbon sources (Olive oil, Triolein, Tributyrin, and Glucose). Eleven candidate reference genes (ACT, GPH1, AGL9, RPB2, SAP1, PGK1, TAF10, UBC13, TFC1, UBP6, and FBA1) were analyzed for their expression patterns and stability. Analysis of gene expression stability was performed using the RefFinder tool, which integrates the geNorm, NormFinder, BestKeeper and Delta-Ct algorithms, and validation of the results was performed through analyzing the expression of a lipase gene, CvLIP4. Analyzing the four treatments together, CvACT and CvRPB2 constituted the best reference gene pair. When treatments are analyzed individually, CvRPB2/CvACT, CvFBA1/CvAGL9, CvPGK1/CvAGL9 and CvACT/CvRPB2 were the best reference gene pairs for the culture media containing olive oil, triolein, tributyrin, and glucose as carbon sources, respectively. These results are essential and form the basis for the development of relative gene expression studies in C. viswanathii, since adequate reference genes are crucial for the reliability of RT-qPCR data.
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Affiliation(s)
- Matheus Martins Daúde
- Laboratory of Molecular Analyses, Department of Life Sciences, Faculty of Medicine, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil
| | - Ronan Cristhian Teixeira
- Laboratory of Biotechnology, Food analyses, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Carlos Henrique Cardon
- Laboratory of Plant Molecular Physiology, Department of Biology, Federal University of Lavras, MG, Brazil
| | - Gessi Carvalho de Araujo Santos
- Laboratory of Molecular Analyses, Department of Life Sciences, Faculty of Medicine, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil
| | - Alex Fernando de Almeida
- Laboratory of Biotechnology, Food analyses, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Department of Biology, Federal University of Lavras, MG, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analyses, Department of Life Sciences, Faculty of Medicine, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil.
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de Souza MR, Teixeira RC, Daúde MM, Augusto ANL, Ságio SA, de Almeida AF, Barreto HG. Comparative assessment of three RNA extraction methods for obtaining high-quality RNA from Candida viswanathii biomass. J Microbiol Methods 2021; 184:106200. [PMID: 33713728 DOI: 10.1016/j.mimet.2021.106200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 11/24/2022]
Abstract
Isolating high quality RNA is a limiting factor in molecular analysis, since it is the base for transcriptional studies. The RNA extraction method can directly affect the RNA quality and quantity, as well as, its overall cost. The industrial importance of the yeast genus Candida in several sectors comes from their capacity to produce Lipases. These enzymes are one of the main metabolites produced by some Candida species, and it has been shown that Candida yeast can biodegrade petroleum hydrocarbons and diesel oil from biosurfactants that they can produce, a feature that turns these organisms into potential combatants for bioremediation techniques. Thus, this study aimed to determine an efficient method for isolating high quality RNA from Candida viswanathii biomass. To achieve this aim, three different RNA extraction methods, TRIzol, Hot Acid Phenol, and CTAB (Cetyltrimethylammonium Bromide), were tested. The three tested methods allowed the isolation of high-quality RNA from C. viswanathii biomass and yielded suitable RNA quantity for carrying out RT-qPCR studies. In addition, all methods displayed high sensitivity for the expression analysis of the CvGPH1 gene through RT-qPCR, with TRIzol and CTAB showing the best results and the CTAB method displaying the best cost-benefit ratio (US$0.35/sample).
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Affiliation(s)
- Micaele Rodrigues de Souza
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Ronan Cristhian Teixeira
- Laboratory of Biotechnology, Food analysis, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Matheus Martins Daúde
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Anderson Neiva Lopes Augusto
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Solange Aparecida Ságio
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Alex Fernando de Almeida
- Laboratory of Biotechnology, Food analysis, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil.
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Espinosa MEÁ, Moreira RO, Lima AA, Ságio SA, Barreto HG, Luiz SLP, Abreu CEA, Yanes-Paz E, Ruíz YC, González-Olmedo JL, Chalfun-Júnior A. Early histological, hormonal, and molecular changes during pineapple (Ananas comosus (L.) Merrill) artificial flowering induction. J Plant Physiol 2017; 209:11-19. [PMID: 27988471 DOI: 10.1016/j.jplph.2016.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
Natural flowering can cause serious scheduling problems in the pineapple (Ananas comosus) industry and increase harvest costs. Pineapple flowering is thought to be triggered by increased ethylene levels and artificial forcing of pineapple flowering is a common practice to promote flowering synchronisation. However, little is known about the early hormonal and molecular changes of pineapple flowering induction and development. Here, we aimed to analyse the molecular, hormonal, and histological changes during artificial pineapple flowering by Ethrel®48 treatment. Histological analyses of the shoot apical meristem, leaf gibberellic acid (GA3), and ethylene quantification were carried out during the first 72h after Ethrel®48 treatment. Expression profiles from ethylene biosynthesis (AcACS2 and AcACO1), gibberellin metabolism (AcGA2-ox1 and AcDELLA1), and flower development (FT-like gene (AcFT), LFY-like gene (AcLFY), and a PISTILLATA-like gene (AcPI)) genes were analysed during the first 24h after Ethrel®48 treatment. Differentiation processes of the shoot apical meristem into flower buds were already present in the first 72h after Ethrel®48 treatment. Ethrel®48 lead to a reduction in GA3 levels, probably triggered by elevated ethylene levels and the positive regulation AcGA2-ox1. AcLFY activation upon Ethrel®48 may also have contributed to the reduction of GA3 levels and, along with the up-regulation of AcPI, are probably associated with the flower induction activation. AcFT and AcDELLA1 do not seem to be regulated by GA3 and ethylene. Decreased GA3 and increased ethylene levels suggest an accumulation of AcDELLA1, which may display an important role in pineapple flowering induction. Thus, this study shows that molecular, hormonal, and histological changes are present right after Ethrel®48 treatment, providing new insights into how pineapple flowering occurs under natural conditions.
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Affiliation(s)
| | - Rafael Oliveira Moreira
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - André Almeida Lima
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | | | - Horllys Gomes Barreto
- Federal University of Tocantins (UFT), Campus Universitário de Gurupi, Gurupi, Tocantins, Brazil
| | | | | | | | | | | | - Antonio Chalfun-Júnior
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil.
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Oliveira DM, Chalfun-Junior A, Chizzotti ML, Barreto HG, Coelho TC, Paiva LV, Coelho CP, Teixeira PD, Schoonmaker JP, Ladeira MM. Expression of genes involved in lipid metabolism in the muscle of beef cattle fed soybean or rumen-protected fat, with or without monensin supplementation. J Anim Sci 2014; 92:5426-36. [PMID: 25403202 DOI: 10.2527/jas.2014-7855] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Degree of unsaturation of fatty acids, which is influenced by lipid source and level of metabolism in the rumen, is a major determinant in how dietary lipids affect genes that regulate beef marbling. A total of 28 Red Norte bulls with an initial live weight of 361±32 kg (P>0.05) were used in a completely randomized experimental design to analyze the expression of genes that are involved in lipid metabolism in the longissimus dorsi (LD) when diets contained soybean grain or rumen-protected fat, with or without monensin. Treatments were arranged as a 2×2 factorial, with 4 treatments and 7 replicates per treatment. Half of the animals that received soybean or rumen-protected fat were supplemented with 230 mg head(-1) d(-1) of monensin. Gene expression was analyzed by reverse-transcription quantitative PCR (RT-qPCR). Expression of sterol regulatory element-binding protein-1c (SREBP-1c) in the LD muscle was not affected by lipid source or monensin (P>0.05). There was an interaction effect (P<0.05) between lipid source and monensin for peroxisome proliferator-activated receptor α (PPAR-α) and stearoyl-CoA desaturase (SCD) expression, where greater gene expression was found in animals fed soybean plus monensin and the lower gene expression was found in animals fed rumen-protected fat plus monensin. Expression of lipoprotein lipase (LPL) and fatty acid-binding protein 4 (FABP4) were greater (P<0.05) in the LD muscle of animals fed soybean. Monensin had no effect on LPL and FABP4 expression when soybean without monensin was fed, but when rumen-protected fat was fed, monensin increased LPL expression and decreased FABP4 expression (P<0.05). Linoleic and arachidonic acids had negative correlations (P<0.05) with the expression of PPAR-α, SCD, FABP4, and LPL genes. PPAR-α gene expression was not correlated with SREBP-1c but was positively correlated with SCD, FABP4, LPL, and glutathione peroxidase (GPX1) gene expression (P<0.001). Lipid sources and monensin interact and alter the expression of PPAR-α, SCD, acetyl CoA carboxylase α (ACACA), LPL, FABP4, and GPX1. These changes in gene expression were most associated with arachidonic and α-linolenic acids and the ability of lipid sources and monensin to increase these fatty acids in tissues.
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Affiliation(s)
- D M Oliveira
- Department of Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - A Chalfun-Junior
- Department of Biology, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - M L Chizzotti
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil, 36.570-000
| | - H G Barreto
- Department of Agricultural Sciences, Universidade Federal de Tocantins, Gurupi, Tocantins, Brazil, 77.402-970
| | - T C Coelho
- Department of Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - L V Paiva
- Department of Chemistry, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - C P Coelho
- Department of Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - P D Teixeira
- Department of Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
| | - J P Schoonmaker
- Department of Animal Science, Purdue University, West Lafayette, IN 47906
| | - M M Ladeira
- Department of Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil, 37.200-000
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