21 results on '"Consiglio, Federica"'
Search Results
2. Terapia cellulare e genica per il trattamento dell’Epidermolisi Bollosa Distrofica Recessiva
- Author
-
Consiglio, Federica
- Subjects
RDEB ,Clinical trial ,Gene therapy ,Terapia genica ,COL7A1 ,Staminali epiteliali ,Trial clinico ,Settore BIO/11 - Biologia Molecolare ,Epidermal stem cells - Published
- 2023
3. A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana
- Author
-
Orsini, Francesco, D'Urzo, Matilde Paino, Inan, Gunsu, Serra, Sara, Oh, Dong-Ha, Mickelbart, Michael V., Consiglio, Federica, Li, Xia, Jeong, Jae Cheol, Yun, Dae-Jin, Bohnert, Hans J., Bressan, Ray A., and Maggio, Albino
- Published
- 2010
4. The Arabidopsis RESURRECTION1 Gene Regulates a Novel Antagonistic Interaction in Plant Defense to Biotrophs and Necrotrophs
- Author
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Mang, Hyung Gon, Laluk, Kristin A., Parsons, Eugene P., Kosma, Dylan K., Cooper, Bruce R., Park, Hyeong Cheol, AbuQamar, Synan, Boccongelli, Claudia, Miyazaki, Saori, Consiglio, Federica, Chilosi, Gabriele, Bohnert, Hans J., Bressan, Ray A., Mengiste, Tesfaye, and Jenks, Matthew A.
- Published
- 2009
- Full Text
- View/download PDF
5. Transcription profiling of laser microdissected microsporocytes in an Arabidopsis mutant (Atmcc1) with enhanced histone acetylation
- Author
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Barra, Lucia, Aiese-Cigliano, Riccardo, Cremona, Gaetana, De Luca, Pasquale, Zoppoli, Pietro, Bressan, Ray A., Consiglio, Federica M., and Conicella, Clara
- Published
- 2012
- Full Text
- View/download PDF
6. Tolerance to abiotic stresses in potato plants: a molecular approach
- Author
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Leone, Antonella, Costa, Antonello, Consiglio, Federica, Massarelli, Immacolata, Dragonetti, Emilia, De Palma, Monica, and Grillo, Stefania
- Published
- 1999
- Full Text
- View/download PDF
7. Histone hyperacetylation affects meiotic recombination and chromosome segregation in Arabidopsis
- Author
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Perrella, Giorgio, Consiglio, Federica M., Aiese-Cigliano, Riccardo, Cremona, Gaetana, Sanchez-Moran, Eugenio, Barra, Lucia, Errico, Angela, Bressan, Ray A., Franklin, Christopher F. H., and Conicella, Clara
- Published
- 2010
- Full Text
- View/download PDF
8. Screening for mutations affecting sexual reproduction after activation tagging inArabidopsis thaliana
- Author
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Perrella, Giorgio, Cremona, Gaetana, Consiglio, Federica, Errico, Angela, Bressan, Ray A., and Conicella, Clara
- Published
- 2006
- Full Text
- View/download PDF
9. Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles
- Author
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Aiese Cigliano Riccardo, Sanseverino Walter, Cremona Gaetana, Ercolano Maria R, Conicella Clara, and Consiglio Federica M
- Subjects
Solanum lycopersicum ,Epigenetics ,Development ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. Results Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. Conclusions In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.
- Published
- 2013
- Full Text
- View/download PDF
10. Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#
- Author
-
Consiglio Federica M, Cremona Gaetana, Sanseverino Walter, Cigliano Riccardo, and Conicella Clara
- Subjects
Evolution ,QH359-425 - Abstract
Abstract Background Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n). Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL) and to highlight the evolution of PSL family in plants. Results Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts. Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean. The analysis of PSLFHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations. Conclusions In this study, we highlight the existence of PSLs throughout Viridaeplantae, from mosses to higher plants. We provide evidence that PSLs occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate PSL gene having a role in 2n pollen that should be deeply investigated. We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.
- Published
- 2011
- Full Text
- View/download PDF
11. Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis.
- Author
-
Termolino, Pasquale, Falque, Matthieu, Aiese Cigliano, Riccardo, Cremona, Gaetana, Paparo, Rosa, Ederveen, Antoine, Martin, Olivier C., Consiglio, Federica M., and Conicella, Clara
- Subjects
HOMOLOGOUS chromosomes ,CHROMOSOME inversions ,CHROMOSOMAL rearrangement ,BOTANISTS ,ARABIDOPSIS - Abstract
Summary: During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis. Significance Statement: This work provides further information into the poorly described phenomenon of the interchromosomal (IC) effect in plants. Indeed, the few studies on this phenomenon in maize date back to the 1960s and 1970s and have low resolution, being limited to a few specific regions and genetic markers. In this paper we underscore the significance for plant scientists of the IC effect during meiosis and provide more detailed data and analyses. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
12. Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.
- Author
-
Tranchida-Lombardo, Valentina, Cigliano, Riccardo Aiese, Anzar, Irantzu, Landi, Simone, Palombieri, Samuela, Colantuono, Chiara, Bostan, Hamed, Termolino, Pasquale, Aversano, Riccardo, Batelli, Giorgia, Cammareri, Maria, Carputo, Domenico, Chiusano, Maria Luisa, Conicella, Clara, Consiglio, Federica, D'Agostino, Nunzio, De Palma, Monica, Di Matteo, Antonio, Grandillo, Silvana, and Sanseverino, Walter
- Abstract
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8M and 56.4M of 30-150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
13. Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles.
- Author
-
Cigliano, Riccardo Aiese, Sanseverino, Walter, Cremona, Gaetana, Ercolano, Maria R., Conicella, Clara, and Consiglio, Federica M.
- Subjects
PLANT genomes ,HISTONE acetyltransferase ,HISTONE deacetylase ,HISTONE demethylases ,METHYLATION ,TOMATOES ,PLANT growth ,ARABIDOPSIS thaliana - Abstract
Background: Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. Results: Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. Conclusions: In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
14. Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#.
- Author
-
Cigliano, Riccardo Aiese, Sanseverino, Walter, Cremona, Gaetana, Consiglio, Federica M., and Conicella, Clara
- Subjects
PALYNOLOGY ,ARABIDOPSIS thaliana ,GENOMICS ,PLANT evolution ,CELL division - Abstract
Background: Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n). Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL) and to highlight the evolution of PSL family in plants. Results: Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts. Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean. The analysis of PSL
FHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations. Conclusions: In this study, we highlight the existence of PSLs throughout Viridaeplantae, from mosses to higher plants. We provide evidence that PSLs occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate PSL gene having a role in 2n pollen that should be deeply investigated. We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function. [ABSTRACT FROM AUTHOR]- Published
- 2011
- Full Text
- View/download PDF
15. The Arabidopsis RESURRECTION1 Gene Regulates a Novel Antagonistic Interaction in Plant Defense to Biotrophs and Necrotrophs.
- Author
-
Hyung Gon Mang, Laluk, Kristin A., Parsons, Eugene P., Dylan K. Kosma, Cooper, Bruce R., Hyeong Cheol Park, AbuQamar, Synan, Boccongelli, Claudia, Miyazaki, Saori, Consiglio, Federica, Chilosi, Gabriele, Bohnert, Hans J., Bressan, Ray A., Mengiste, Tesfaye, and Jenks, Matthew A.
- Subjects
ARABIDOPSIS thaliana ,PLANT defenses ,PLANT physiology research ,ERYSIPHE cichoracearum ,BOTRYTIS cinerea ,PLANT plasma membranes ,JASMONIC acid - Abstract
We report a role for the Arabidopsis (Arabidopsis thaliana) RESURRECTION1 (RST1) gene in plant defense. The rst1 mutant exhibits enhanced susceptibility to the biotrophic fungal pathogen Erysiphe cichoracearum but enhanced resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. RST1 encodes a novel protein that localizes to the plasma membrane and is predicted to contain 11 transmembrane domains. Disease responses in rst1 correlate with higher levels of jasmonic acid GA) and increased basal and B. cinerea-induced expression of the plant defensin PDF1.2 gene but reduced E. cichoracearum-inducible salicylic acid levels and expression of pathogenesis-related genes PR1 and PR2. These results are consistent with rst1's varied resistance and susceptibility to pathogens of different life styles. Cuticular lipids, both cutin monomers and cuticular waxes, on rst1 leaves were significantly elevated, indicating a role for RST1 in the suppression of leaf cuticle lipid synthesis. The rst1 cuticle exhibits normal permeability, however, indicating that the disease responses of rst1 are not due to changes in this cuticle property. Double mutant analysis revealed that the coil mutation (causing defective JA signaling) is completely epistatic to rst1, whereas the ein2 mutation (causing defective ethylene signaling) is partially epistatic to rst1, for resistance to B. cinerea. The rst1 mutation thus defines a unique combination of disease responses to biotrophic and necrotrophic fungi in that it antagonizes salicylic acid-dependent defense and enhances JA-mediated defense through a mechanism that also controls cuticle synthesis. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
16. Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace
- Author
-
Riccardo Aiese Cigliano, Riccardo Aversano, Antonio Di Matteo, Samuela Palombieri, Pasquale Termolino, Claudia Angelini, Hamed Bostan, Maria Cammareri, Federica Maria Consiglio, Floriana Della Ragione, Rosa Paparo, Vladimir Totev Valkov, Antonella Vitiello, Domenico Carputo, Maria Luisa Chiusano, Maurizio D’Esposito, Silvana Grandillo, Maria Rosaria Matarazzo, Luigi Frusciante, Nunzio D’Agostino, Clara Conicella, Cigliano, Riccardo Aiese, Aversano, Riccardo, Di Matteo, Antonio, Palombieri, Samuela, Termolino, Pasquale, Angelini, Claudia, Bostan, Hamed, Cammareri, Maria, Consiglio, Federica Maria, Ragione, Floriana Della, Paparo, Rosa, Valkov, Vladimir Totev, Vitiello, Antonella, Carputo, Domenico, Chiusano, Maria Luisa, D'Esposito, Maurizio, Grandillo, Silvana, Matarazzo, Maria Rosaria, Frusciante, Luigi, D'Agostino, Nunzio, and Conicella, Clara
- Subjects
post-harvest ,epigenetics ,Genetics ,food and beverages ,Plant Science ,multi-omics ,Horticulture ,Biochemistry ,Tomato ,Article ,Biotechnology - Abstract
In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as “Piennolo del Vesuvio”, all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.
- Published
- 2022
17. Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#.
- Author
-
Cigliano, Riccardo Aiese, Sanseverino, Walter, Cremona, Gaetana, Consiglio, Federica M., and Conicella, Clara
- Subjects
- *
PALYNOLOGY , *ARABIDOPSIS thaliana , *GENOMICS , *PLANT evolution , *CELL division - Abstract
Background: Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n). Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL) and to highlight the evolution of PSL family in plants. Results: Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts. Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean. The analysis of PSLFHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations. Conclusions: In this study, we highlight the existence of PSLs throughout Viridaeplantae, from mosses to higher plants. We provide evidence that PSLs occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate PSL gene having a role in 2n pollen that should be deeply investigated. We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
18. Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits
- Author
-
Pasquale Termolino, Marina Tucci, Clara Conicella, Irantzu Anzar, Silvana Grandillo, Nunzio D’Agostino, Maria Cammareri, Samuela Palombieri, Chiara Colantuono, Valentina Tranchida-Lombardo, Simone Landi, Monica De Palma, Riccardo Aiese Cigliano, Walter Sanseverino, Domenico Carputo, Riccardo Aversano, Federica Consiglio, Antonio Di Matteo, Giorgia Batelli, Stefania Grillo, Hamed Bostan, Maria Luisa Chiusano, Tranchida-lombardo, Valentina, Aiese Cigliano, Riccardo, Anzar, Irantzu, Landi, Simone, Palombieri, Samuela, Colantuono, Chiara, Bostan, Hamed, Termolino, Pasquale, Aversano, Riccardo, Batelli, Giorgia, Cammareri, Maria, Carputo, Domenico, Chiusano, Maria Luisa, Conicella, Clara, Consiglio, Federica, De Palma, Monica, Di Matteo, Antonio, Grandillo, Silvana, Sanseverino, Walter, Tucci, Marina, and Grillo, Stefania
- Subjects
0106 biological sciences ,0301 basic medicine ,genomic platform ,Single-nucleotide polymorphism ,Genomics ,Genes, Plant ,01 natural sciences ,Genome ,DNA sequencing ,03 medical and health sciences ,Solanum lycopersicum ,Stress, Physiological ,Botany ,Genetics ,Molecular Biology ,Gene ,traditional varieties ,next generation sequencing ,Whole genome sequencing ,Polymorphism, Genetic ,Base Sequence ,Whole Genome Sequencing ,biology ,food and beverages ,General Medicine ,Full Papers ,biology.organism_classification ,Solanum pimpinellifolium ,030104 developmental biology ,Fruit ,Genome, Plant ,traditional varieties, SNPs, next generation sequencing, genomic platform ,SNPs ,010606 plant biology & botany ,Reference genome - Abstract
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8 M and 56.4 M of 30–150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.
- Published
- 2018
19. Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace.
- Author
-
Cigliano RA, Aversano R, Di Matteo A, Palombieri S, Termolino P, Angelini C, Bostan H, Cammareri M, Consiglio FM, Della Ragione F, Paparo R, Valkov VT, Vitiello A, Carputo D, Chiusano ML, D'Esposito M, Grandillo S, Matarazzo MR, Frusciante L, D'Agostino N, and Conicella C
- Abstract
In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as "Piennolo del Vesuvio", all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
20. Clonal analysis of human clonogenic keratinocytes.
- Author
-
Enzo E, Cattaneo C, Consiglio F, Polito MP, Bondanza S, and De Luca M
- Subjects
- Cells, Cultured, Genetic Therapy methods, Humans, Regenerative Medicine, Keratinocytes, Stem Cells
- Abstract
Regenerative medicine has its roots in harnessing stem cells for permanent restoration of damaged or diseased tissues. The first procedure for the transplantation of epidermal cultures in massive full-thickness burns was established in the 1980s. Since then, epithelial stem cell-based therapies have been further developed in cell and gene therapy protocols aimed at restoring visual acuity in severe ocular burns and treating patients affected by genetic skin diseases, as Epidermolysis Bullosa. The clinical success of these Advanced Therapy Medicinal Products (ATMPs) requires the presence of a defined number of epithelial stem cells in the grafts, detected as holoclone-forming cells. To date, the most trustworthy method to identify and measure holoclones in a culture is the clonal analysis of clonogenic keratinocytes. Here we describe in detail how to perform such a clonal analysis and identify each epidermal clonal type., (Copyright © 2022 Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
21. Evolution of parallel spindles like genes in plants and highlight of unique domain architecture#.
- Author
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Cigliano RA, Sanseverino W, Cremona G, Consiglio FM, and Conicella C
- Subjects
- Alternative Splicing, Amino Acid Sequence, Arabidopsis genetics, Cloning, Molecular, DNA, Plant genetics, Gene Dosage, Genes, Plant, Likelihood Functions, Molecular Sequence Data, Plant Proteins genetics, Polyploidy, Protein Structure, Secondary, Sequence Alignment, Sequence Analysis, DNA, Glycine max genetics, Arabidopsis Proteins genetics, Evolution, Molecular, Multigene Family, Phylogeny, Solanum tuberosum genetics
- Abstract
Background: Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n). Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL) and to highlight the evolution of PSL family in plants., Results: Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts.Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean.The analysis of PSLFHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations., Conclusions: In this study, we highlight the existence of PSLs throughout Viridaeplantae, from mosses to higher plants. We provide evidence that PSLs occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate PSL gene having a role in 2n pollen that should be deeply investigated.We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.
- Published
- 2011
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