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Cappelli K, Mecocci S, Porceddu A, Albertini E, Giontella A, Miglio A, Silvestrelli M, Verini Supplizi A, Marconi G, Capomaccio S. Genome-wide epigenetic modifications in sports horses during training as an adaptation phenomenon. Sci Rep 2023; 13:18786. [PMID: 37914824 PMCID: PMC10620398 DOI: 10.1038/s41598-023-46043-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
With his bicentennial breeding history based on athletic performance, the Thoroughbred horse can be considered the equine sport breed. Although genomic and transcriptomic tools and knowledge are at the state of the art in equine species, the epigenome and its modifications in response to environmental stimuli, such as training, are less studied. One of the major epigenetic modifications is cytosine methylation at 5' of DNA molecules. This crucial biochemical modification directly mediates biological processes and, to some extent, determines the organisms' phenotypic plasticity. Exercise indeed affects the epigenomic state, both in humans and in horses. In this study, we highlight, with a genome-wide analysis of methylation, how the adaptation to training in the Thoroughbred can modify the methylation pattern throughout the genome. Twenty untrained horses, kept under the same environmental conditions and sprint training regimen, were recruited, collecting peripheral blood at the start of the training and after 30 and 90 days. Extracted leukocyte DNA was analyzed with the methylation content sensitive enzyme ddRAD (MCSeEd) technique for the first time applied to animal cells. Approximately one thousand differently methylated genomic regions (DMRs) and nearby genes were called, revealing that methylation changes can be found in a large part of the genome and, therefore, referable to the physiological adaptation to training. Functional analysis via GO enrichment was also performed. We observed significant differences in methylation patterns throughout the training stages: we hypothesize that the methylation profile of some genes can be affected early by training, while others require a more persistent stimulus.
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Affiliation(s)
- Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Samanta Mecocci
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy.
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy.
| | - Andrea Porceddu
- Department of Agraria, University of Sassari, 06123, Sassari, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Arianna Miglio
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Andrea Verini Supplizi
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
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Monterisi S, Zuluaga MYA, Porceddu A, Cesco S, Pii Y. The Application of High-Resolution Melting Analysis to trnL (UAA) Intron Allowed a Qualitative Identification of Apple Juice Adulterations. Foods 2023; 12:foods12071437. [PMID: 37048258 PMCID: PMC10093500 DOI: 10.3390/foods12071437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Food authenticity plays a pivotal role in the modern age since an increased consumers awareness has led them to pay more attention to food commodities. For this reason, it is important to have reliable and fast techniques able to detect possible adulterations in food, which affect qualitative and economic value. Therefore, the aim of this study was to detect possible adulterations in apple juice from others fruit species (i.e., pear, peach, and kiwi) combining DNA barcoding approach, using trnL (UAA) intron, with high resolution melting analysis (HRMA). A preliminary phylogenetic analysis, using sequences retrieved by the GenBank, confirmed the discriminatory power of trnL (UAA) intron among the four fruit species examined. Moreover, the sequencing of the trnL (UAA) fragments obtained from apple, pear, peach, and kiwi, demonstrated the suitability of an inner shorter sequence, P6 loop, to differentiate the considered species. The HRMA coupled with trnL (UAA) intron allowed discrimination among the four fruits but provided incomplete results for juices. Whereas the HRMA targeting the P6 loop amplicons confirmed the suitability of the technique to qualitatively distinguish fruit juices composed by the combination of apple/pear and apple/peach. However, the impossibility of discriminating apple/kiwi juices from the pure kiwi sample highlighted limitations, most likely related to the DNA extraction process. This hypothesis was further confirmed by analyzing DNA blends obtained by combining nucleic acids extracted from pure matrixes (i.e., apple and kiwi fruits). In this specific case, the application of HRMA allowed both qualitative and quantitative assessment of the samples.
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Panara F, Passeri V, Lopez L, Porceddu A, Calderini O, Paolocci F. Functional Characterization of MtrGSTF7, a Glutathione S-Transferase Essential for Anthocyanin Accumulation in Medicago truncatula. Plants 2022; 11:plants11101318. [PMID: 35631744 PMCID: PMC9147808 DOI: 10.3390/plants11101318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
Flavonoids are essential compounds widespread in plants and exert many functions such as defence, definition of organ colour and protection against stresses. In Medicago truncatula, flavonoid biosynthesis and accumulation is finely regulated in terms of tissue specificity and induction by external factors, such as cold and other stresses. Among flavonoids, anthocyanin precursors are synthesised in the cytoplasm, transported to the tonoplast, then imported into the vacuole for further modifications and storage. In the present work, we functionally characterised MtrGSTF7, a phi-class glutathione S-transferase involved in anthocyanin transport to the tonoplast. The mtrgstf7 mutant completely lost the ability to accumulate anthocyanins in leaves both under control and anthocyanin inductive conditions. On the contrary, this mutant showed an increase in the levels of soluble proanthocyanidins (Pas) in their seeds with respect to the wild type. By complementation and expression data analysis, we showed that, differently from A. thaliana and similarly to V. vinifera, transport of anthocyanin and proanthocyanidins is likely carried out by different GSTs belonging to the phi-class. Such functional diversification likely results from the plant need to finely tune the accumulation of diverse classes of flavonoids according to the target organs and developmental stages.
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Affiliation(s)
- Francesco Panara
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development, (ENEA), 75026 Rotondella, MT, Italy; (F.P.); (L.L.)
| | - Valentina Passeri
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, PG, Italy; (V.P.); (F.P.)
| | - Loredana Lopez
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development, (ENEA), 75026 Rotondella, MT, Italy; (F.P.); (L.L.)
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Viale Italia, 39a, 07100 Sassari, SS, Italy;
| | - Ornella Calderini
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, PG, Italy; (V.P.); (F.P.)
- Correspondence: ; Tel.: +39-075-501-4858
| | - Francesco Paolocci
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, PG, Italy; (V.P.); (F.P.)
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Lopez L, Perrella G, Calderini O, Porceddu A, Panara F. Genome-Wide Identification of Histone Modification Gene Families in the Model Legume Medicago truncatula and Their Expression Analysis in Nodules. Plants 2022; 11:plants11030322. [PMID: 35161303 PMCID: PMC8838541 DOI: 10.3390/plants11030322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/22/2023]
Abstract
Histone methylation and acetylation are key processes in the epigenetic regulation of plant growth, development, and responses to environmental stimuli. The genes encoding for the enzymes that are responsible for these chromatin post-translational modifications, referred to as histone modification genes (HMGs), have been poorly investigated in Leguminosae species, despite their importance for establishment and activity of nitrogen-fixing nodules. In silico analysis of Medicago truncatula HMGs identified 81 histone methyltransferases, 46 histone demethylases, 64 histone acetyltransferases, and 15 histone deacetylases. MtHMGs were analyzed for their structure and domain composition, and some combinations that were not yet reported in other plant species were identified. Genes have been retrieved from M. truncatula A17 and R108 genotypes as well as M. sativa CADL and Zhongmu No.1; the gene number and distribution were compared with Arabidopsis thaliana. Furthermore, by analyzing the expression data that were obtained at various developmental stages and in different zones of nitrogen-fixing nodules, we identified MtHMG loci that could be involved in nodule development and function. This work sets a reference for HMG genomic organization in legumes which will be useful for functional investigation that is aimed at elucidating HMGs involvement in nodule development and symbiotic nitrogen fixation.
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Affiliation(s)
- Loredana Lopez
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Giorgio Perrella
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Ornella Calderini
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, Italy
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Viale Italia, 39a, 07100 Sassari, Italy;
| | - Francesco Panara
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
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Tini F, Beccari G, Marconi G, Porceddu A, Sulyok M, Gardiner DM, Albertini E, Covarelli L. Identification of Putative Virulence Genes by DNA Methylation Studies in the Cereal Pathogen Fusarium graminearum. Cells 2021; 10:cells10051192. [PMID: 34068122 PMCID: PMC8152758 DOI: 10.3390/cells10051192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 01/17/2023] Open
Abstract
DNA methylation mediates organisms’ adaptations to environmental changes in a wide range of species. We investigated if a such a strategy is also adopted by Fusarium graminearum in regulating virulence toward its natural hosts. A virulent strain of this fungus was consecutively sub-cultured for 50 times (once a week) on potato dextrose agar. To assess the effect of subculturing on virulence, wheat seedlings and heads (cv. A416) were inoculated with subcultures (SC) 1, 23, and 50. SC50 was also used to re-infect (three times) wheat heads (SC50×3) to restore virulence. In vitro conidia production, colonies growth and secondary metabolites production were also determined for SC1, SC23, SC50, and SC50×3. Seedling stem base and head assays revealed a virulence decline of all subcultures, whereas virulence was restored in SC50×3. The same trend was observed in conidia production. The DNA isolated from SC50 and SC50×3 was subject to a methylation content-sensitive enzyme and double-digest, restriction-site-associated DNA technique (ddRAD-MCSeEd). DNA methylation analysis indicated 1024 genes, whose methylation levels changed in response to the inoculation on a healthy host after subculturing. Several of these genes are already known to be involved in virulence by functional analysis. These results demonstrate that the physiological shifts following sub-culturing have an impact on genomic DNA methylation levels and suggest that the ddRAD-MCSeEd approach can be an important tool for detecting genes potentially related to fungal virulence.
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Affiliation(s)
- Francesco Tini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.T.); (G.B.); (E.A.); (L.C.)
| | - Giovanni Beccari
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.T.); (G.B.); (E.A.); (L.C.)
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.T.); (G.B.); (E.A.); (L.C.)
- Correspondence:
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Viale Italia, 39a, 07100 Sassari, Italy;
| | - Micheal Sulyok
- Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Applied Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse, 20, A-3430 Tulln, Austria;
| | - Donald M. Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia;
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.T.); (G.B.); (E.A.); (L.C.)
| | - Lorenzo Covarelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.T.); (G.B.); (E.A.); (L.C.)
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Mascagni F, Usai G, Cavallini A, Porceddu A. Structural characterization and duplication modes of pseudogenes in plants. Sci Rep 2021; 11:5292. [PMID: 33674668 PMCID: PMC7935947 DOI: 10.1038/s41598-021-84778-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.
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Affiliation(s)
- Flavia Mascagni
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gabriele Usai
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli studi di Sassari, Via Enrico de Nicola 1, 07100, Sassari, Italy.
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Di Marsico M, Cerruti E, Comino C, Porceddu A, Acquadro A, Capomaccio S, Marconi G, Albertini E. MCSeEd (Methylation Context Sensitive Enzyme ddRAD): A New Method to Analyze DNA Methylation. Methods Mol Biol 2020; 2093:47-64. [PMID: 32088888 DOI: 10.1007/978-1-0716-0179-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Methylation context sensitive enzyme ddRAD (MCSeEd) is a NGS-based method for genome-wide investigations of DNA methylation at different contexts requiring only low to moderate sequencing depth. It is particularly useful for identifying methylation changes in experimental systems challenged by biotic or abiotic stresses or at different developmental stages.
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Affiliation(s)
- Marco Di Marsico
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy.
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
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Garau G, Porceddu A, Sanna M, Silvetti M, Castaldi P. Municipal solid wastes as a resource for environmental recovery: Impact of water treatment residuals and compost on the microbial and biochemical features of As and trace metal-polluted soils. Ecotoxicol Environ Saf 2019; 174:445-454. [PMID: 30852309 DOI: 10.1016/j.ecoenv.2019.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 01/22/2019] [Revised: 02/27/2019] [Accepted: 03/03/2019] [Indexed: 05/04/2023]
Abstract
In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg-1). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and β-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.
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Affiliation(s)
- Giovanni Garau
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy.
| | - Andrea Porceddu
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Monica Sanna
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Margherita Silvetti
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Paola Castaldi
- Dipartimento di Chimica e Farmacia, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.
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Viglietti G, Galla G, Porceddu A, Barcaccia G, Curk F, Luro F, Scarpa GM. Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives. Plants (Basel) 2019; 8:plants8040083. [PMID: 30935148 PMCID: PMC6524030 DOI: 10.3390/plants8040083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/24/2019] [Accepted: 03/28/2019] [Indexed: 12/04/2022]
Abstract
Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between C. aurantium (as seed bearer) and C. medica (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree.
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Affiliation(s)
- Grazia Viglietti
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
| | - Giulio Galla
- Laboratory of Genomics, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Padova, Italy.
| | - Andrea Porceddu
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
| | - Gianni Barcaccia
- Laboratory of Genomics, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Padova, Italy.
| | - Frank Curk
- Unite Mixte de Recherche Amelioration Genetique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France.
| | - Francois Luro
- Unite Mixte de Recherche Amelioration Genetique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France.
| | - Grazia Maria Scarpa
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
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Muresu R, Porceddu A, Sulas L, Squartini A. Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes. Microbiol Res 2019; 221:10-14. [PMID: 30825937 DOI: 10.1016/j.micres.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Received: 12/18/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/30/2023]
Abstract
The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae. 63 isolates from 60 surface-sterilized nodules were analyzed by ARDRA and 16S rDNA sequencing. The official nitrogen-fixing symbiont Rhizobium sullae was found only in 25 nodules out of 60. The remaining nodules did not yield culturable rhizobia but a number of different endophytic genera including Pseudomonas sp. (17 nodules), Microbacterium sp. (15 nodules), Pantoea agglomerans (5 nodules). The situation appears therefore a hybrid between what is commonly observed in other Mediterranean legumes occurring only in wild status (featuring non-culturable rhizobia and arrays of culturable endophytes within nodules), as opposed to cropped legumes (endowed with fully culturable rhizobia and minimal endophytic occurrence). These findings, within a species bridging the ecology between native and cropped conditions, suggest insights on the relative importance of endophytic co-occupancy vs. true N-fixing symbiont culturability within nodules. The latter trait thus appears to accompany the domestication path of plants with a main trade-off of renouncing to interactions with a diversity of endophytic co-invaders; the relationships with those being critical in the non-cropped status. In fact, endophytes are known to promote plant growth in harsh conditions, which can be particularly stressful in the Mediterranean due to drought, highly calcareous soils, and pathogens outbreaks.
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Affiliation(s)
- Rosella Muresu
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, University of Sassari, Viale Italia 1, 07100, Sassari, Italy
| | - Leonardo Sulas
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Università 16, Legnaro, Padova, Italy.
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Rapposelli E, Rigoldi MP, Satta D, Delpiano D, Secci S, Porceddu A. Genetic, Phenotypic, and Commercial Characterization of an Almond Collection from Sardinia. Plants (Basel) 2018; 7:plants7040086. [PMID: 30326629 PMCID: PMC6313889 DOI: 10.3390/plants7040086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/04/2018] [Accepted: 10/12/2018] [Indexed: 11/16/2022]
Abstract
Background: Recent nutritional and medical studies have associated the regular consumption of almonds with a wide range of health benefits. As a consequence, kernel quality has become an important goal for breeding, considering not only the chemical composition conferring a specific organoleptic quality but also physical traits related to industrial processing. Methods: We characterized an almond collection from Sardinia through analysis of 13 morpho-physiological traits and eight essential oil profiles. The genetic structure of the collection was studied by analyzing the polymorphism of 11 simple sequence repeats (SSR). Results: Both commercial and phenotypic traits showed wide ranges of variation. Most genotypes were early flowering with low yield potential. Several genotypes showed moderate to high yield and very interesting oil compositions of kernels. Based on 11 SSR profiles and Bayesian clustering, the Sardinian cultivars were assigned to groups which were differentiated for several agronomic and commercial traits. Conclusions: Several cultivars showed a high kernel oil content and high oleic to linoleic content ratio. Based on morphological traits, we propose that some of the analyzed cultivars could be interesting for industrial applications. Finally, we highlight the importance of characterizing early blooming cultivars for sites which are experiencing a rise in mean temperatures due to the effects of global climate changes.
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Affiliation(s)
- Emma Rapposelli
- Servizio per la Ricerca in Arboricoltura, Agenzia per la Ricerca in Agricoltura della Regione Autonoma della Sardegna (AGRIS Sardegna), Via Demartini 244, 07100 Sassari, Italy.
| | - Maria Pia Rigoldi
- Servizio per la Ricerca in Arboricoltura, Agenzia per la Ricerca in Agricoltura della Regione Autonoma della Sardegna (AGRIS Sardegna), Via Demartini 244, 07100 Sassari, Italy.
| | - Daniela Satta
- Servizio per la Ricerca in Arboricoltura, Agenzia per la Ricerca in Agricoltura della Regione Autonoma della Sardegna (AGRIS Sardegna), Via Demartini 244, 07100 Sassari, Italy.
| | - Donatella Delpiano
- Servizio Ricerca nelle Filiere Olivicolo-Olearia e Viti-Enologica, Agenzia per la Ricerca in Agricoltura della Regione Autonoma della Sardegna (AGRIS Sardegna), Strada Statale 196 Villasor-Villacidro, Km. 14.600, 09034 Villasor, Italy.
| | - Sara Secci
- Servizio per la Ricerca in Arboricoltura, Agenzia per la Ricerca in Agricoltura della Regione Autonoma della Sardegna (AGRIS Sardegna), Via Demartini 244, 07100 Sassari, Italy.
| | - Andrea Porceddu
- Agronomia, Coltivazioni Erbacee e Genetica, Dipartimento di Agraria, Università degli Studi di Sassari, via Enrico De Nicola, 07100 Sassari, Italy.
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12
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Camiolo S, Toome-Heller M, Aime MC, Haridas S, Grigoriev IV, Porceddu A, Mannazzu I. An analysis of codon bias in six red yeast species. Yeast 2018; 36:53-64. [PMID: 30264407 DOI: 10.1002/yea.3359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 06/08/2018] [Revised: 09/10/2018] [Accepted: 09/23/2018] [Indexed: 11/11/2022] Open
Abstract
Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.
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Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Merje Toome-Heller
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Ilaria Mannazzu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
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Porceddu A, Sanna M, Prota VA, Schianchi N, Mercenaro L, Nieddu G, Camiolo S. First Report of Grapevine Asteroid Mosaic-Associated Virus Infecting Grapevines (Vitis vinifera) in Italy. Plant Dis 2018; 102:PDIS03180460PDN. [PMID: 30078366 DOI: 10.1094/pdis-03-18-0460-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- A Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - M Sanna
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - V A Prota
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - N Schianchi
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - L Mercenaro
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - G Nieddu
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
| | - S Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100, Sassari, Italy
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14
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Camiolo S, Porceddu A. corseq: fast and efficient identification of favoured codons from next generation sequencing reads. PeerJ 2018; 6:e5099. [PMID: 30013827 PMCID: PMC6035725 DOI: 10.7717/peerj.5099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Background Optimization of transgene expression can be achieved by designing coding sequences with the synonymous codon usage of genes which are highly expressed in the host organism. The identification of the so-called “favoured codons” generally requires the access to either the genome or the coding sequences and the availability of expression data. Results Here we describe corseq, a fast and reliable software for detecting the favoured codons directly from RNAseq data without prior knowledge of genomic sequence or gene annotation. The presented tool allows the inference of codons that are preferentially used in highly expressed genes while estimating the transcripts abundance by a new kmer based approach. corseq is implemented in Python and runs under any operating system. The software requires the Biopython 1.65 library (or later versions) and is available under the ‘GNU General Public License version 3’ at the project webpage https://sourceforge.net/projects/corseq/files. Conclusion corseq represents a faster and easy-to-use alternative for the detection of favoured codons in non model organisms.
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15
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Marche MG, Camiolo S, Porceddu A, Ruiu L. Survey of Brevibacillus laterosporus insecticidal protein genes and virulence factors. J Invertebr Pathol 2018; 155:38-43. [DOI: 10.1016/j.jip.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/27/2018] [Accepted: 05/09/2018] [Indexed: 10/16/2022]
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Landolfo S, Ianiri G, Camiolo S, Porceddu A, Mulas G, Chessa R, Zara G, Mannazzu I. CAR gene cluster and transcript levels of carotenogenic genes in Rhodotorula mucilaginosa. Microbiology (Reading) 2018; 164:78-87. [DOI: 10.1099/mic.0.000588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sara Landolfo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Via Francesco de Sanctis, 86100 Campobasso, Italy
- Present address: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Salvatore Camiolo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Andrea Porceddu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuliana Mulas
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Rossella Chessa
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giacomo Zara
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Ilaria Mannazzu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
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17
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Ariani P, Vandelle E, Wong D, Giorgetti A, Porceddu A, Camiolo S, Polverari A. Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine. J Vis Exp 2017. [PMID: 29286420 DOI: 10.3791/56626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the prediction of family functions based on several features, such as the presence of sequence motifs or of particular sites for post-translational modification and the expression profile of family members in different conditions. This work describes a detailed protocol for gene family characterization. Here, the procedure is applied to the characterization of the Arabidopsis Tóxicos in Levadura (ATL) E3 ubiquitin ligase family in grapevine. The methods include the genome-wide identification of family members, the characterization of gene localization, structure, and duplication, the analysis of conserved protein motifs, the prediction of protein localization and phosphorylation sites as well as gene expression profiling across the family in different datasets. Such procedure, which could be extended to further analyses depending on experimental purposes, could be applied to any gene family in any plant species for which genomic data are available, and it provides valuable information to identify interesting candidates for functional studies, giving insights into the molecular mechanisms of plant adaptation to their environment.
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Affiliation(s)
- Pietro Ariani
- Dipartimento di Biotecnologie, Università degli Studi di Verona
| | - Elodie Vandelle
- Dipartimento di Biotecnologie, Università degli Studi di Verona;
| | - Darren Wong
- Ecology and Evolution, Research School of Biology, The Australian National University
| | | | - Andrea Porceddu
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari
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18
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Camiolo S, Porru C, Benítez-Cabello A, Rodríguez-Gómez F, Calero-Delgado B, Porceddu A, Budroni M, Mannazzu I, Jiménez-Díaz R, Arroyo-López FN. Genome overview of eight Candida boidinii strains isolated from human activities and wild environments. Stand Genomic Sci 2017; 12:70. [PMID: 29213357 PMCID: PMC5712119 DOI: 10.1186/s40793-017-0281-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, Sassari, Italy
| | - Cinzia Porru
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, Sassari, Italy
| | - Antonio Benítez-Cabello
- Food Biotechnology Department, Instituto de la Grasa (C.S.I.C.), University Campus Pablo de Olavide, Building 46, Crta. de Utrera km 1, 41013 Seville, Spain
| | - Francisco Rodríguez-Gómez
- Food Biotechnology Department, Instituto de la Grasa (C.S.I.C.), University Campus Pablo de Olavide, Building 46, Crta. de Utrera km 1, 41013 Seville, Spain
| | - Beatríz Calero-Delgado
- Food Biotechnology Department, Instituto de la Grasa (C.S.I.C.), University Campus Pablo de Olavide, Building 46, Crta. de Utrera km 1, 41013 Seville, Spain
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, Sassari, Italy
| | - Marilena Budroni
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, Sassari, Italy
| | - Ilaria Mannazzu
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, Sassari, Italy
| | - Rufino Jiménez-Díaz
- Food Biotechnology Department, Instituto de la Grasa (C.S.I.C.), University Campus Pablo de Olavide, Building 46, Crta. de Utrera km 1, 41013 Seville, Spain
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa (C.S.I.C.), University Campus Pablo de Olavide, Building 46, Crta. de Utrera km 1, 41013 Seville, Spain
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19
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Mercenaro L, Nieddu G, Porceddu A, Pezzotti M, Camiolo S. Sequence Polymorphisms and Structural Variations among Four Grapevine ( Vitis vinifera L.) Cultivars Representing Sardinian Agriculture. Front Plant Sci 2017; 8:1279. [PMID: 28775732 PMCID: PMC5517397 DOI: 10.3389/fpls.2017.01279] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/06/2017] [Indexed: 05/04/2023]
Abstract
The genetic diversity among grapevine (Vitis vinifera L.) cultivars that underlies differences in agronomic performance and wine quality reflects the accumulation of single nucleotide polymorphisms (SNPs) and small indels as well as larger genomic variations. A combination of high throughput sequencing and mapping against the grapevine reference genome allows the creation of comprehensive sequence variation maps. We used next generation sequencing and bioinformatics to generate an inventory of SNPs and small indels in four widely cultivated Sardinian grape cultivars (Bovale sardo, Cannonau, Carignano and Vermentino). More than 3,200,000 SNPs were identified with high statistical confidence. Some of the SNPs caused the appearance of premature stop codons and thus identified putative pseudogenes. The analysis of SNP distribution along chromosomes led to the identification of large genomic regions with uninterrupted series of homozygous SNPs. We used a digital comparative genomic hybridization approach to identify 6526 genomic regions with significant differences in copy number among the four cultivars compared to the reference sequence, including 81 regions shared between all four cultivars and 4953 specific to single cultivars (representing 1.2 and 75.9% of total copy number variation, respectively). Reads mapping at a distance that was not compatible with the insert size were used to identify a dataset of putative large deletions with cultivar Cannonau revealing the highest number. The analysis of genes mapping to these regions provided a list of candidates that may explain some of the phenotypic differences among the Bovale sardo, Cannonau, Carignano and Vermentino cultivars.
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Affiliation(s)
- Luca Mercenaro
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Giovanni Nieddu
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università degli Studi di VeronaVerona, Italy
| | - Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
- *Correspondence: Salvatore Camiolo,
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20
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Ariani P, Regaiolo A, Lovato A, Giorgetti A, Porceddu A, Camiolo S, Wong D, Castellarin S, Vandelle E, Polverari A. Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members. Sci Rep 2016; 6:38260. [PMID: 27910910 PMCID: PMC5133618 DOI: 10.1038/srep38260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023] Open
Abstract
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.
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Affiliation(s)
- Pietro Ariani
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Alice Regaiolo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Arianna Lovato
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Alejandro Giorgetti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Andrea Porceddu
- Università degli Studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy
| | - Salvatore Camiolo
- Università degli Studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy
| | - Darren Wong
- Wine Research Centre, University of British Columbia, 326-2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Simone Castellarin
- Wine Research Centre, University of British Columbia, 326-2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Elodie Vandelle
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Annalisa Polverari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
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Abstract
BACKGROUND Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations. RESULTS Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection. CONCLUSIONS Altools is fast, reliable and easy to use for the mining of NGS data. The software package also attempts to link identified polymorphisms and structural variants to their biological functions thus providing more valuable information than similar tools.
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Affiliation(s)
- Salvatore Camiolo
- Università degli studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy.
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Sydney, Australia.
| | - Andrea Porceddu
- Università degli studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy.
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22
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Ma MY, Che XR, Porceddu A, Niu DK. Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evol Biol 2015; 15:286. [PMID: 26678305 PMCID: PMC4683709 DOI: 10.1186/s12862-015-0567-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background Spliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, plants, and fungi. The slime mold Dictyostelium belongs to a supergroup of eukaryotes not covered in previous studies. Results We found 441 precise intron losses in Dictyostelium discoideum and 202 precise intron losses in Dictyostelium purpureum. Consistent with these observations, Dictyostelium discoideum was found to have significantly more copies of reverse transcriptase genes than Dictyostelium purpureum. We also found that the lost introns are significantly further from the 5′ end of genes than the conserved introns. Adjacent introns were prone to be lost simultaneously in Dictyostelium discoideum. In both Dictyostelium species, the exonic sequences flanking lost introns were found to have a significantly higher GC content than those flanking conserved introns. Together, these observations support a reverse-transcription model of intron loss in which intron losses were caused by gene conversion between genomic DNA and cDNA reverse transcribed from mature mRNA. We also identified two imprecise intron losses in Dictyostelium discoideum that may have resulted from genomic deletions. Ninety-eight putative intron gains were also observed. Consistent with previous studies of other lineages, the source sequences were found in only a small number of cases, with only two instances of intron gain identified in Dictyostelium discoideum. Conclusions Although they diverged very early from animals and fungi, Dictyostelium species have similar mechanisms of intron loss. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0567-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-Yue Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. .,Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Xun-Ru Che
- The High School Affiliated to Renmin University of China, Beijing, 100080, China.
| | - Andrea Porceddu
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy.
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. .,Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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23
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Abstract
Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.
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Affiliation(s)
- S Camiolo
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
| | - S Melito
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
| | - A Porceddu
- Dipartimento di Agraria, SACEG, Università degli Studi di Sassari, Sassari, Italy
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Milia G, Camiolo S, Avesani L, Porceddu A. The dynamic loss and gain of introns during the evolution of the Brassicaceae. Plant J 2015; 82:915-924. [PMID: 25899207 DOI: 10.1111/tpj.12860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 02/18/2015] [Revised: 04/02/2015] [Accepted: 04/09/2015] [Indexed: 06/04/2023]
Abstract
Sequence comparison allows the detailed analysis of evolution at the nucleotide and amino acid levels, but much less information is known about the structural evolution of genes, i.e. how the number, length and distribution of introns change over time. We constructed a parsimonious model for the evolutionary rate of intron loss (IL) and intron gain (IG) within the Brassicaceae and found that IL/IG has been highly dynamic, with substantial differences between and even within lineages. The divergence of the Brassicaceae lineages I and II marked a dramatic change in the IL rate, with the common ancestor of lineage I losing introns three times more rapidly than the common ancestor of lineage II. Our data also indicate a subsequent declining trend in the rate of IL, although in Arabidopsis thaliana introns continue to be lost at approximately the ancestral rate. Variations in the rate of IL/IG within lineage II have been even more remarkable. Brassica rapa appears to have lost introns approximately 15 times more rapidly than the common ancestor of B. rapa and Schenkiella parvula, and approximately 25 times more rapidly than its sister species Eutrema salsugineum. Microhomology was detected at the splice sites of several dynamic introns suggesting that the non-homologous end-joining and double-strand break repair is a common pathway underlying IL/IG in these species. We also detected molecular signatures typical of mRNA-mediated IL, but only in B. rapa.
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Affiliation(s)
- Giampiera Milia
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Salvatore Camiolo
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Andrea Porceddu
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
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Rigoldi MP, Rapposelli E, De Giorgio D, Resta P, Porceddu A. Genetic diversity in two Italian almond collections. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2014.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Camiolo S, Melito S, Milia G, Porceddu A. Seforta, an integrated tool for detecting the signature of selection in coding sequences. BMC Res Notes 2014; 7:240. [PMID: 24739143 PMCID: PMC4022393 DOI: 10.1186/1756-0500-7-240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The majority of amino acid residues are encoded by more than one codon, and a bias in the usage of such synonymous codons has been repeatedly demonstrated. One assumption is that this phenomenon has evolved to improve the efficiency of translation by reducing the time required for the recruitment of isoacceptors. The most abundant tRNA species are preferred at sites on the protein which are key for its functionality, a behavior which has been termed "translational accuracy". Although observed in many species, as yet no public domain software has been made available for its quantification. FINDINGS We present here Seforta (Selection for Translational Accuracy), a program designed to quantify translational accuracy. It searches for synonymous codon usage bias in both conserved and non-conserved regions of coding sequences and computes a cumulative odds ratio and a Z-score. The specification of a set of preferred codons is desirable, but the program can also generate these. Finally, a randomization protocol calculates the probability that preferred codon combinations could have arisen by chance. CONCLUSIONS Seforta is the first public domain program able to quantify translational accuracy. It comes with a simple graphical user interface and can be readily installed and adjusted to the user's requirements.
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Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy.
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Abstract
Little is known about the natural selection of synonymous codons within the coding sequences of plant genes. We analyzed the distribution of synonymous codons within plant coding sequences and found that preferred codons tend to encode the more conserved and functionally important residues of plant proteins. This was consistent among several synonymous codon families and applied to genes with different expression profiles and functions. Most of the randomly chosen alternative sets of codons scored weaker associations than the actual sets of preferred codons, suggesting that codon position within plant genes and codon usage bias have coevolved to maximize translational accuracy. All these findings are consistent with the mistranslation-induced protein misfolding theory, which predicts the natural selection of highly preferred codons more frequently at sites where translation errors could compromise protein folding or functionality. Our results will provide an important insight in future studies of protein folding, molecular evolution, and transgene design for optimal expression.
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Affiliation(s)
- Andrea Porceddu
- Dipartimento di Agraria, Sezione di Agronomia e Coltivazione Erbacee Genetica-SACEG, Università degli studi di Sassari, Italy.
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Melito S, Sias A, Petretto GL, Chessa M, Pintore G, Porceddu A. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum. PLoS One 2013; 8:e79043. [PMID: 24260149 PMCID: PMC3832510 DOI: 10.1371/journal.pone.0079043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/25/2013] [Indexed: 11/25/2022] Open
Abstract
Background Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. Methods H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. Key results The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. Conclusions The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.
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Affiliation(s)
- Sara Melito
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
- Centro Interdipartimentale per la Conservazione e Valorizzazione della Biodiversità Vegetale, Loc. Surigheddu, Sassari, Italy
- * E-mail:
| | - Angela Sias
- Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy
| | - Giacomo L. Petretto
- Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy
| | - Mario Chessa
- Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy
| | - Giorgio Pintore
- Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy
- Centro Interdipartimentale per la Conservazione e Valorizzazione della Biodiversità Vegetale, Loc. Surigheddu, Sassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
- Centro Interdipartimentale per la Conservazione e Valorizzazione della Biodiversità Vegetale, Loc. Surigheddu, Sassari, Italy
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Abstract
Background General Feature Format (GFF) files are used to store genome features such as genes, exons, introns, primary transcripts etc. Although many software packages (i.e. ab initio gene prediction programs) can annotate features by using such a standard, a small number of tools have been developed to extract the corresponding sequence information from the original genome. However the present tools do not execute either a quality control or a customizable filter of the annotated features is available. Findings gff2sequence is a program that extracts nucleotide/protein sequences from a genomic multifasta by using the information provided by a general feature format file. While a graphical user interface makes this software very easy to use, a C++ algorithm allows high performance together with low hardware demand. The software also allows the extraction of the genic portions such as the untranslated and the coding sequences. Moreover a highly customizable quality control pipeline can be used to deal with anomalous splicing sites, incorrect open reading frames and not canonical characters within the retrieved sequences. Conclusions gff2sequence is a user friendly program that allows the generation of highly customizable sequence datasets by processing a general feature format file. The presence of a wide range of quality filters makes this tool also suitable for refining the ab initio gene predictions.
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Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy.
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Fasoli M, Dal Santo S, Zenoni S, Tornielli GB, Farina L, Zamboni A, Porceddu A, Venturini L, Bicego M, Murino V, Ferrarini A, Delledonne M, Pezzotti M. The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program. Plant Cell 2012; 24:3489-505. [PMID: 22948079 PMCID: PMC3480284 DOI: 10.1105/tpc.112.100230] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/06/2012] [Accepted: 08/20/2012] [Indexed: 05/18/2023]
Abstract
We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed ∼91% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.
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Affiliation(s)
- Marianna Fasoli
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Silvia Dal Santo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Sara Zenoni
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | | | - Lorenzo Farina
- Dipartimento di Informatica e Sistemistica Antonio Ruberti, Università degli Studi di Roma La Sapienza, 00185 Rome, Italy
| | - Anita Zamboni
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Andrea Porceddu
- Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Luca Venturini
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Manuele Bicego
- Dipartimento di Informatica, Università degli Studi di Verona, 37134 Verona, Italy
| | | | - Alberto Ferrarini
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
- Address correspondence to
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Marconi G, Albertini E, Mari A, Palazzo P, Porceddu A, Raggi L, Bolis L, Lancioni H, Palomba A, Lucentini L, Lanfaloni L, Marcucci F, Falcinelli M, Panara F. In planta expression of a mature Der p 1 allergen isolated from an Italian strain of Dermatophagoides pteronyssinus. Transgenic Res 2012; 21:523-35. [PMID: 21904913 DOI: 10.1007/s11248-011-9551-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 08/25/2011] [Indexed: 10/17/2022]
Abstract
European (Dermatophagoides pteronyssinus) and American (Dermatophagoides farinae) house dust mite species are considered the most common causes of asthma and allergic symptoms worldwide. Der p 1 protein, one of the main allergens of D. pteronyssinus, is found in high concentration in mites faecal pellets, which can became easily airborne and, when inhaled, can cause perennial rhinitis and bronchial asthma. Here we report the isolation of the Der p 1 gene from an Italian strain of D. pteronyssinus and the PVX-mediated expression of its mature form (I-rDer p 1) in Nicotiana benthamiana plants. Human sera from characterized allergic patients were used for IgE binding inhibition assays to test the immunological reactivity of I-rDer p 1 produced in N. benthamiana plants. The binding properties of in planta produced I-rDer p 1 versus the IgE of patients sera were comparable to those obtained on Der p 1 preparation immobilized on a microarray. In this paper we provide a proof of concept for the production of an immunologically active form of Der p 1 using a plant viral vector. These results pave the way for the development of diagnostic allergy tests based on in planta produced allergens.
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Affiliation(s)
- Gianpiero Marconi
- Dipartimento di Biologia Applicata, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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Abstract
Genomic DNA sequences display compositional heterogeneity on many scales. In this paper we analyzed tendencies and anomalies in the occurence of mono, di and trinucleotides in structural regions of plant genes. Representation of these trends as a function of position along genic sequences highlighted compositional features peculiar of either monocots or eudicots that were remarkably uniform within these two evolutionary clades. The most evident of these features appeared in the form of gradient of base content along the direction of transcription. The robustness of such a representation was validated in sequences sub-datasets generated considering structural and compositional features such as total length of cds, overall GC content and genic orientation in the genome. Piecewise regression analyses indicated that the gradients could be conveniently approximated to a two segmented model where a first region featuring a steep slope is followed by a second segment fitting a milder variation. In general, monocots species showed steeper segments than eudicots. The guanine gradient was the most distinctive feature between the two evolutionary clades, being moderately increasing in eudicots and firmly decreasing in monocots. Single gene investigation revealed that a high proportion of genes show compositional trends compatible with a segmented model suggesting that these features are essential attributes of gene organization. Dinucleotide and trinucleotide biases were referred to expectation based on a random union of the component elements. The average bias at dinucleotide level identified a significant undererpresentation of some dinucleotide and the overrepresention of others. The bias at trinucleotide level was on average low. Finally, the analysis of bryophyte coding sequences showed mononucleotide, dinucleotide and trinucleotide compositional trends resembling those of higher plants. This finding suggested that the emergenge of compositional bias is an ancient event in evolution which was already present at the time of land conquest by green plants.
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Affiliation(s)
- Andrea Porceddu
- Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari, Sassari, Italy.
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Carelli M, Biazzi E, Panara F, Tava A, Scaramelli L, Porceddu A, Graham N, Odoardi M, Piano E, Arcioni S, May S, Scotti C, Calderini O. Medicago truncatula CYP716A12 Is a Multifunctional Oxidase Involved in the Biosynthesis of Hemolytic Saponins. The Plant Cell 2011; 23:3070-81. [PMID: 21821776 PMCID: PMC3180811 DOI: 10.1105/tpc.111.087312] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Abstract
Saponins, a group of glycosidic compounds present in several plant species, have aglycone moieties that are formed using triterpenoid or steroidal skeletons. In spite of their importance as antimicrobial compounds and their possible benefits for human health, knowledge of the genetic control of saponin biosynthesis is still poorly understood. In the Medicago genus, the hemolytic activity of saponins is related to the nature of their aglycone moieties. We have identified a cytochrome P450 gene (CYP716A12) involved in saponin synthesis in Medicago truncatula using a combined genetic and biochemical approach. Genetic loss-of-function analysis and complementation studies showed that CYP716A12 is responsible for an early step in the saponin biosynthetic pathway. Mutants in CYP716A12 were unable to produce hemolytic saponins and only synthetized soyasaponins, and were thus named lacking hemolytic activity (lha). In vitro enzymatic activity assays indicate that CYP716A12 catalyzes the oxidation of β-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of triterpenic saponin biosynthetic pathway: squalene cyclization, β-amyrin oxidation, and glycosylation. The analysis of CYP716A12 expression in planta is reported together with the sapogenin content in different tissues and stages. This article provides evidence for CYP716A12 being a key gene in hemolytic saponin biosynthesis.
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Affiliation(s)
- Maria Carelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Elisa Biazzi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Francesco Panara
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Aldo Tava
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Laura Scaramelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Andrea Porceddu
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Neil Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Miriam Odoardi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Efisio Piano
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Sergio Arcioni
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Sean May
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Carla Scotti
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Ornella Calderini
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
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Porceddu A, Panara F, Calderini O, Molinari L, Taviani P, Lanfaloni L, Scotti C, Carelli M, Scaramelli L, Bruschi G, Cosson V, Ratet P, de Larembergue H, Duc G, Piano E, Arcioni S. An Italian functional genomic resource for Medicago truncatula. BMC Res Notes 2008; 1:129. [PMID: 19077311 PMCID: PMC2633015 DOI: 10.1186/1756-0500-1-129] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 12/15/2008] [Indexed: 12/24/2022] Open
Abstract
Background Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes. Findings Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States.
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Affiliation(s)
- Andrea Porceddu
- CNR Istituto di Genetica Vegetale Perugia, via Madonna Alta, 130 Perugia, Italy.
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Belaj A, Muñoz-Diez C, Baldoni L, Porceddu A, Barranco D, Satovic Z. Genetic diversity and population structure of wild olives from the North-Western Mediterranean assessed by SSR markers. Ann Bot 2007; 100:449-58. [PMID: 17613587 PMCID: PMC2533604 DOI: 10.1093/aob/mcm132] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS This study examines the pattern of genetic variability and genetic relationships of wild olive (Olea europaea subsp. europaea var. sylvestris) populations in the north-western Mediterranean. Recent bottleneck events are also assessed and an investigation is made of the underlying population structure of the wild olive populations. METHODS The genetic variation within and between 11 wild olive populations (171 individuals) was analysed with eight microsatellite markers. Conventional and Bayesian-based analyses were applied to infer genetic structure and define the number of gene pools in wild olive populations. KEY RESULTS Bayesian model-based clustering identified four gene pools, which was in overall concordance with the Factorial Correspondence Analysis and Fitch-Margoliash tree. Two gene pools were predominantly found in southern Spain and Italian islands, respectively, in samples gathered from undisturbed forests of the typical Mediterranean climate. The other two gene pools were mostly detected in the north-eastern regions of Spain and in continental Italy and belong to the transition region between the temperate and Mediterranean climate zones. CONCLUSIONS On the basis of these results, it can be assumed that the population structure of wild olives from the north-western Mediterranean partially reflects the evolutionary history of these populations, although hybridization between true oleasters and cultivated varieties in areas of close contact between the two forms must be assumed as well. The study indicates a degree of admixture in all the populations, and suggests some caution regarding genetic differentiation at the population level, making it difficult to identify clear-cut genetic boundaries between candidate areas containing either genuinely wild or feral germplasm.
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Affiliation(s)
- Angjelina Belaj
- Centro Alameda del Obispo, IFAPA, Avda Menéndez Pidal s/n 14083, Córdoba, Spain.
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Sarri V, Baldoni L, Porceddu A, Cultrera NGM, Contento A, Frediani M, Belaj A, Trujillo I, Cionini PG. Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 2007; 49:1606-15. [PMID: 17426775 DOI: 10.1139/g06-126] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Twelve simple sequence repeat (SSR) loci were used to differentiate among 118 cultivars sampled in several countries of the Mediterranean basin and to analyze the genetic structure of olive cultivar gene pools. The markers were found to have high discrimination power. On average, with a single assay it was possible to discriminate 96% of the pairwise comparisons and, with a combination of 3 loci, virtually all cultivars were distinguished. The SSR markers were also tested for their ability to assign cultivars to their geographic population of origin. A selection of 6 loci was found to maximize assignment accuracy, correctly reallocating up to 75.4% of cultivars to their population of origin. Because of the confusion surrounding the origin of most olive cultivars, their molecular identification and ascertainment of origin will be extremely useful for germplasm management and breeding.
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Affiliation(s)
- V Sarri
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
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Avesani L, Marconi G, Morandini F, Albertini E, Bruschetta M, Bortesi L, Pezzotti M, Porceddu A. Stability of Potato virus X expression vectors is related to insert size: implications for replication models and risk assessment. Transgenic Res 2007; 16:587-97. [PMID: 17216546 DOI: 10.1007/s11248-006-9051-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 10/17/2006] [Indexed: 12/28/2022]
Abstract
We investigated the stability of expression constructs based on Potato virus X (PVX) as a function of insert length. Five different inserts ranging in length from 261 to 1,758 bp (human proinsulin, murine interleukin-10, HIV-1 nef, petunia expansin-1 and human gad65) were expressed using a PVX vector in Nicotiana benthamiana plants for three sequential passages. Using a competitive RT-PCR approach we demonstrated that insert-deletion could occur in the first infection cycle for all inserts, but that this was much more likely to be the case for longer ones. This suggested a negative correlation between insert length and vector stability. Sequence analysis of the deleted constructs suggested that recombination usually occurred at sites close to the duplicated sub-genomic promoter, but in a smaller number of cases the foreign gene itself was probably involved, resulting in partially deleted constructs containing transgene fragments. The implications of these results in the context of recombinant protein expression and its risks are discussed.
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Affiliation(s)
- Linda Avesani
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
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Baldoni L, Tosti N, Ricciolini C, Belaj A, Arcioni S, Pannelli G, Germana MA, Mulas M, Porceddu A. Genetic structure of wild and cultivated olives in the central Mediterranean basin. Ann Bot 2006. [PMID: 16935868 DOI: 10.1093/aob/mcl/178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.
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Baldoni L, Tosti N, Ricciolini C, Belaj A, Arcioni S, Pannelli G, Germana MA, Mulas M, Porceddu A. Genetic structure of wild and cultivated olives in the central Mediterranean basin. Ann Bot 2006; 98:935-942. [PMID: 16935868 DOI: 10.1093/aob/mc1178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.
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Baldoni L, Tosti N, Ricciolini C, Belaj A, Arcioni S, Pannelli G, Germana MA, Mulas M, Porceddu A. Genetic structure of wild and cultivated olives in the central Mediterranean basin. Ann Bot 2006; 98:935-42. [PMID: 16935868 PMCID: PMC2803593 DOI: 10.1093/aob/mcl178] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.
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Marconi G, Albertini E, Barone P, De Marchis F, Lico C, Marusic C, Rutili D, Veronesi F, Porceddu A. In planta production of two peptides of the Classical Swine Fever Virus (CSFV) E2 glycoprotein fused to the coat protein of potato virus X. BMC Biotechnol 2006; 6:29. [PMID: 16792815 PMCID: PMC1534020 DOI: 10.1186/1472-6750-6-29] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 06/22/2006] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Classical Swine Fever (CSFV) is one of the most important viral infectious diseases affecting wild boars and domestic pigs. The etiological agent of the disease is the CSF virus, a single stranded RNA virus belonging to the family Flaviviridae. All preventive measures in domestic pigs have been focused in interrupting the chain of infection and in avoiding the spread of CSFV within wild boars as well as interrupting transmission from wild boars to domestic pigs. The use of plant based vaccine against CSFV would be advantageous as plant organs can be distributed without the need of particular treatments such as refrigeration and therefore large areas, populated by wild animals, could be easily covered. RESULTS We report the in planta production of peptides of the classical swine fever (CSF) E2 glycoprotein fused to the coat protein of potato virus X. RT-PCR studies demonstrated that the peptide encoding sequences are correctly retained in the PVX construct after three sequential passage in Nicotiana benthamiana plants. Sequence analysis of RT-PCR products confirmed that the epitope coding sequences are replicated with high fidelity during PVX infection. Partially purified virions were able to induce an immune response in rabbits. CONCLUSION Previous reports have demonstrated that E2 synthetic peptides can efficiently induce an immunoprotective response in immunogenized animals. In this work we have showed that E2 peptides can be expressed in planta by using a modified PVX vector. These results are particularly promising for designing strategies for disease containment in areas inhabited by wild boars.
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Affiliation(s)
- Gianpiero Marconi
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Emidio Albertini
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Pierluigi Barone
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
- University of Illinois at Urbana-Champaign, College of Agricultural, Consumer and Environmental Sciences, Department of Crop Sciences, 289 Edward R. Madigan Laboratory, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Francesca De Marchis
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
- Istituto di Genetica Vegetale, Sezione di Perugia, Via Madonna Alta 130, 06100 Perugia, Italy
| | | | | | - Domenico Rutili
- Istituto Sperimentale Zooprofilattico dell'Umbria e delle Marche, Sezione di Perugia, Italy
| | - Fabio Veronesi
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Andrea Porceddu
- Dipartimento di Biologia vegetale e Biotecnologie Agroambientali e Zootecniche, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
- Istituto di Genetica Vegetale, Sezione di Perugia, Via Madonna Alta 130, 06100 Perugia, Italy
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Cappelli K, Porceddu A, Verini-Supplizi A, Capomaccio S, Marchis FD, Falcinelli M, Gaiti A, Silvestrelli M. cDNA AFLP-based techniques for studying transcript profiles in horses. Res Vet Sci 2005; 79:105-12. [PMID: 15924927 DOI: 10.1016/j.rvsc.2004.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Revised: 11/08/2004] [Accepted: 11/10/2004] [Indexed: 11/30/2022]
Abstract
The identification of differentially expressed genes is a fundamental prerequisite for understanding the molecular regulation of most physiological and pathological processes. Among the procedures employed to compare mRNA populations, those that are gel-based appear to hold great promise and are considered excellent tools for studying gene expression in species, such as the equine one, for which little genomic information is available. In the present study, we evaluated two techniques for studying mRNA profiles in horse tissue, one referred to the cDNA-amplified fragment length polymorphism (AFLP) that we called C-AFLP (classical cDNA-AFLP) protocol and the other to ordered differential display (ODD) with some modifications that we named S-AFLP (systematic cDNA-AFLP). Both techniques can be applied in live animals because of the small amount of sample required. We applied the S-AFLP to investigate horse transcript profile modifications during physical exercise. We found two transcripts that are mostly expressed during exercise and immediately after the end of it.
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Affiliation(s)
- K Cappelli
- Centro di Studio del Cavallo Sportivo, Facoltà di Medicina Veterinaria, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
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Albertini E, Marconi G, Reale L, Barcaccia G, Porceddu A, Ferranti F, Falcinelli M. SERK and APOSTART. Candidate genes for apomixis in Poa pratensis. Plant Physiol 2005; 138:2185-99. [PMID: 16024690 PMCID: PMC1183406 DOI: 10.1104/pp.105.062059] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Seed production generally requires the mating of opposite sex gametes. Apomixis, an asexual mode of reproduction, avoids both meiotic reduction and egg fertilization. The essential feature of apomixis is that an embryo is formed autonomously by parthenogenesis from an unreduced egg of an embryo sac generated through apomeiosis. If apomixis were well understood and harnessed, it could be exploited to indefinitely propagate superior hybrids or specific genotypes bearing complex gene sets. A more profound knowledge of the mechanisms that regulate reproductive events would contribute fundamentally to understanding the genetic control of the apomictic pathway. In Poa pratensis, we isolated and characterized two genes, PpSERK (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE) and APOSTART. These full-length genes were recovered by rapid amplification of cDNA ends and their temporal and spatial expression patterns were assessed by reverse transcription-polymerase chain reaction and in situ hybridization, respectively. The expression of PpSERK and APOSTART differed in apomictic and sexual genotypes. Their putative role in cell-signaling transduction cascades and trafficking events required during sporogenesis, gametogenesis, and embryogenesis in plants is reported and discussed. We propose that, in nucellar cells of apomictic genotypes, PpSERK is the switch that channels embryo sac development and that it may also redirect signaling gene products to compartments other than their typical ones. The involvement of APOSTART in meiosis and programmed cell death is also discussed.
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Affiliation(s)
- Emidio Albertini
- Department of Plant Biology and Agro-Environmental and Animal Biotechnology, University of Perugia, 06121 Perugia, Italy.
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Huber CG, Walcher W, Timperio AM, Troiani S, Porceddu A, Zolla L. Multidimensional proteomic analysis of photosynthetic membrane proteins by liquid extraction-ultracentrifugation-liquid chromatography-mass spectrometry. Proteomics 2004; 4:3909-20. [PMID: 15449339 DOI: 10.1002/pmic.200400823] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The membrane protein components of photosystem I (PSI) and II (PSII) from different species were prefractionated by liquid extraction and sucrose gradient ultracentrifugation and subsequently analyzed by reversed-phase high-performance liquid chromatography-electrospray ionization-mass spectrometry (RP-HPLC-ESI-MS) using poly-(styrene-divinylbenzene)-based monolithic capillary columns. The analytical method was shown to be very flexible and enabled the identification of antenna proteins as well as most of the proteins of the reaction center from PSI and PSII in various plant species with few RP-HPLC-ESI-MS analyses necessitating only minor adaptations in the gradients of acetonitrile in 0.05% aqueous trifluoroacetic acid. The membrane proteins, ranging in molecular mass (Mr) from 4196 (I protein) to more than 80,000 (PSI A/B) as well as isoforms were identified on the basis of their intact Mr and comparison with Mr deduced from known DNA or protein sequences. High quality mass spectra enabled the identification and quantitation of the nonphosphorylated and phosphorylated reaction center subunits D1, D2, and CP43 of PSII, containing five to seven membrane-spanning alpha-helices. Because of its high flexibility and suitability for proteins having a very wide range of Mr and hydrophobicities, the method is generally applicable to the analysis of complex mixtures of membrane proteins.
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Affiliation(s)
- Christian G Huber
- Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, Saarbrücken, Germany.
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Abstract
In spite of the economical relevance of polyploid crops, genetic mapping of these species has been relatively overlooked. This is because of intrinsic difficulties such as the uncertainty of the chromosome behavior at meiosis I and the need for very large segregating populations. An important, yet underestimated issue, in mapping polyploids is the choice of the molecular marker system. An ideal molecular marker system for polyploid mapping should maximize the percentage of single dose markers (SDMs) detected and the possibility of recognizing allelic markers. In the present work, the marker index for genetic mapping (MIgm) of M-AFLP is compared with that of AFLP and SAMPL. M-AFLPs have the highest MIgm values (22 vs. 18.5 of SAMPL and 9.83 of AFLP) mostly because of their high power to detect polymorphism. Owing to their prevalent codominant inheritance, it is proposed that M-AFLP can be used for the preliminary identification of hom(e)ologous groups.
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Affiliation(s)
- Emidio Albertini
- Department of Plant Biology and Agro-environmental Biotechnology, University of Perugia, Italy
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Zenoni S, Reale L, Tornielli GB, Lanfaloni L, Porceddu A, Ferrarini A, Moretti C, Zamboni A, Speghini A, Ferranti F, Pezzotti M. Downregulation of the Petunia hybrida alpha-expansin gene PhEXP1 reduces the amount of crystalline cellulose in cell walls and leads to phenotypic changes in petal limbs. Plant Cell 2004; 16:295-308. [PMID: 14742876 PMCID: PMC341904 DOI: 10.1105/tpc.018705] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 12/03/2003] [Indexed: 05/18/2023]
Abstract
The expansins comprise a family of proteins that appear to be involved in the disruption of the noncovalent bonds between cellulose microfibrils and cross-linking glycans, thereby promoting wall creep. To understand better the expansion process in Petunia hybrida (petunia) flowers, we isolated a cDNA corresponding to the PhEXP1 alpha-expansin gene of P. hybrida. Evaluation of the tissue specificity and temporal expression pattern demonstrated that PhEXP1 is preferentially expressed in petal limbs during development. To determine the function of PhEXP1, we used a transgenic antisense approach, which was found to cause a decrease in petal limb size, a reduction in the epidermal cell area, and alterations in cell wall morphology and composition. The diminished cell wall thickness accompanied by a reduction in crystalline cellulose indicates that the activity of PhEXP1 is associated with cellulose metabolism. Our results suggest that expansins play a role in the assembly of the cell wall by affecting either cellulose synthesis or deposition.
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MESH Headings
- Cell Size/physiology
- Cell Wall/genetics
- Cell Wall/physiology
- Cellulose/biosynthesis
- Cellulose/metabolism
- Cloning, Molecular
- DNA, Antisense/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Flowers/genetics
- Flowers/growth & development
- Flowers/metabolism
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Petunia/genetics
- Petunia/growth & development
- Petunia/metabolism
- Phenotype
- Plant Epidermis/genetics
- Plant Epidermis/ultrastructure
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Sequence Analysis, DNA
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Affiliation(s)
- Sara Zenoni
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, 37134 Verona, Italy
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Simoncelli F, Sorbolini S, Fagotti A, Di Rosa I, Porceddu A, Pascolini R. Molecular characterization and expression of a divergent α-tubulin in planarian Schmidtea polychroa. ACTA ACUST UNITED AC 2003; 1629:26-33. [PMID: 14522077 DOI: 10.1016/s0167-4781(03)00159-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report the cloning and sequencing of a cDNA from planarian Schmidtea polychroa (Platyhelminthes, Turbellaria, Tricladida) encoding for an unusual tubulin isoform (SpTub-1) which is specifically expressed in testis. Sequence comparison of SpTub-1 with other known tubulins reveals that it has the highest homology with alpha-tubulins, even though the analysis of the molecular features shows that this isoform is significantly divergent. Hybridization of SpTub-1 to restriction-digested genomic DNA to Southern blotting produced a multiple banding pattern indicating that in planarian, a tubulin multigene family exists. Using in situ hybridization, we showed that the transcript is specifically detectable in planarian testis, suggesting that it may play a role in spermatogenesis.
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Affiliation(s)
- Francesca Simoncelli
- Department of Cellular and Molecular Biology, University of Perugia, Via Pascoli, 06123 Perugia, Italy
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Avesani L, Falorni A, Tornielli GB, Marusic C, Porceddu A, Polverari A, Faleri C, Calcinaro F, Pezzotti M. Improved in planta expression of the human islet autoantigen glutamic acid decarboxylase (GAD65). Transgenic Res 2003; 12:203-12. [PMID: 12739888 DOI: 10.1023/a:1022947726557] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The smaller isoform of the enzyme glutamic acid decarboxylase (GAD65) is a major islet autoantigen in autoimmune type 1 diabetes mellitus (T1DM). Transgenic plants expressing human GAD65 (hGAD65) are a potential means of direct oral administration of the islet autoantigen in order to induce tolerance and prevent clinical onset of disease. We have previously reported the successful generation of transgenic tobacco and carrot that express immunoreactive, full-length hGAD65. In the present study, we tested the hypothesis that the expression levels of recombinant hGAD65 in transgenic plants can be increased by targeting the enzyme to the plant cell cytosol and by mediating expression through the potato virus X (PVX) vector. By substituting the NH2-terminal region of hGAD65 with a homologous region of rat GAD67, a chimeric GAD67(1-87)/GAD65(88-585) molecule was expressed in transgenic tobacco plants. Immunolocalization analysis showed that immunoreactive GAD67/65 was found in the plant cell cytosol. By using a radio-immuno assay with human serum from a GAD65 autoantibody-positive T1DM patient, the highest expression level of the recombinant GAD67/65 protein was estimated to be 0.19% of the total soluble protein, compared to only 0.04% of wild-type hGAD65. Transient expression of wild-type, full-length hGAD65 in N. benthamiana mediated by PVX infection was associated with expression levels of immunoreactive protein as high as 2.2% of total soluble protein. This substantial improvement of the expression of hGAD65 in plants paves the way for immunoprevention studies of oral administration of GAD65-containing transgenic plant material in animal models of spontaneous autoimmune diabetes.
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Affiliation(s)
- Linda Avesani
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie 15, 37134, Verona, Italy
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Reale L, Porceddu A, Lanfaloni L, Moretti C, Zenoni S, Pezzotti M, Romano B, Ferranti F. Patterns of cell division and expansion in developing petals of Petunia hybrida. ACTA ACUST UNITED AC 2002. [DOI: 10.1007/s00497-002-0150-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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