title: Validation of reference genes for quantitative real-time PCR in Périgord black truffle (Tuber melanosporum) developmental stages.
abstract: The symbiotic fungus Tuber melanosporum Vittad. (Périgord black truffle) belongs to the Ascomycota and forms mutualistic symbiosis with tree and shrub roots. This truffle has a high value in a global market and is cultivated in many countries of both hemispheres. The publication of the T. melanosporum genome has given researchers unique opportunities to learn more about the biology of the fungus. Real-time quantitative PCR (qRT-PCR) is a definitive technique for quantitating differences in transcriptional gene expression levels between samples. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. These housekeeping genes must show stable expression under given experimental conditions for the qRT-PCR results to be accurate. Unfortunately, there are no studies on the stability of housekeeping genes used in T. melanosporum development. In this study, we present a morphological and microscopical classification of the developmental stages of T. melanosporum fruit body, and investigate the expression levels of 12 candidate reference genes (18S rRNA; 5.8S rRNA; Elongation factor 1-alpha; Elongation factor 1-beta; α-tubulin; 60S ribosomal protein L29; β-tubulin; 40S ribosomal protein S1; 40S ribosomal protein S3; Glucose-6-phosphate dehydrogenase; β-actin; Ubiquitin-conjugating enzyme). To evaluate the suitability of these genes as endogenous controls, five software-based approaches and one web-based comprehensive tool (RefFinder) were used to analyze and rank the tested genes. We demonstrate here that the 18S rRNA gene shows the most stable expression during T. melanosporum development and that a set of three genes, 18S rRNA, Elongation factor 1-alpha and 40S ribosomal protein S3, is the most suitable to normalize qRT-PCR data from all the analyzed developmental stages; conversely, 18S rRNA, Glucose-6-phosphate dehydrogenase and Elongation factor 1-alpha are the most suitable genes for fruiting body developmental stages.
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. Electronic address: osvaldo.zarivi@univaq.it.
authors.forename: Osvaldo
authors.initials: O
authors.lastname: Zarivi
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Cesare
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Ragnelli
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Pierpaolo
authors.initials: P
authors.lastname: Aimola
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Leonardi
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Bonfigli
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Colafarina
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Poma
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Miranda
authors.affiliation: Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Pacioni
mesh_terms: D001203:Ascomycota / Q000737:chemistry / Q000235:genetics*; D048690:Fruiting Bodies, Fungal / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D005954:Glucosephosphate Dehydrogenase / Q000378:metabolism; D020648:Peptide Elongation Factor 1 / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012269:Ribosomal Proteins; D012984:Software; D013559:Symbiosis
chemical_list: C094814:EEF1A1 protein, human; C503234:EEF1A2 protein, human; D020648:Peptide Elongation Factor 1; D012269:Ribosomal Proteins; C015494:ribosomal protein S1; D005954:Glucosephosphate Dehydrogenase
keywords: Developmental stage; Reference gene; Truffle; Tuber melanosporum; qRT-PCR analysis