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2. A Comparison of Prognostic Factors in a Large Cohort of In-Hospital and Out-of-Hospital Cardiac Arrest Patients

Author

Soloperto, Rossana, Magni, Federica, Farinella, Anita, Gouvêa Bogossian, Elisa, Peluso, Lorenzo, De Luca, Nicola, Taccone, Fabio, Annoni, Filippo, Soloperto, Rossana, Magni, Federica, Farinella, Anita, Gouvêa Bogossian, Elisa, Peluso, Lorenzo, De Luca, Nicola, Taccone, Fabio, and Annoni, Filippo

Abstract

We investigated independent factors predicting neurological outcome and death, comparing in-hospital (IHCA) and out-of-hospital cardiac arrest (OHCA) patients. The study was conducted in the mixed 34-bed Intensive Care Department at the Hôpital Universitaire de Bruxelles (HUB), Belgium. All adult consecutive cardiac arrest (CA) survivors were included between 2004 and 2022. For all patients, demographic data, medical comorbidities, CA baseline characteristics, treatments received during Intensive Care Unit stay, in-hospital major complications, and neurological outcome at three months after CA, using the Cerebral Performance Category (CPC) scale, were collected. In the multivariable analysis, in the IHCA group (n = 540), time to return of spontaneous circulation (ROSC), older age, unwitnessed CA, higher lactate on admission, asystole as initial rhythm, a non-cardiac cause of CA, the occurrence of shock, the occurrence of acute kidney injury (AKI), and the presence of previous neurological disease and of liver cirrhosis were independent predictors of an unfavorable neurological outcome. Among patients with OHCA (n = 567), time to ROSC, older age, higher lactate level on admission, unwitnessed CA, asystole or pulseless electrical activity (PEA) as initial rhythm, the occurrence of shock, a non-cardiac cause of CA, and a previous neurological disease were independent predictors of an unfavorable neurological outcome. To conclude, in our large cohort of mixed IHCA and OHCA patients, we observed numerous factors independently associated with a poor neurological outcome, with minimal differences between the two groups, reflecting the greater vulnerability of hospitalized patients., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2024

3. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Author

Scalabrin, Simone, Toniutti, Lucile, Di Gaspero, Gabriele, Scaglione, Davide, Magris, Gabriele, Vidotto, Michele, Pinosio, Sara, Cattonaro, Federica, Magni, Federica, Jurman, Irena, Cerutti, Mario, Suggi Liverani, Furio, Navarini, Luciano, Del Terra, Lorenzo, Pellegrino, Gloria, Ruosi, Manuela Rosanna, Vitulo, Nicola, Valle, Giorgio, Pallavicini, Alberto, Graziosi, Giorgio, Klein, Patricia E., Bentley, Nolan, Murray, Seth, Solano, William, Al Hakimi, Amin, Schilling, Timothy, Montagnon, Christophe, Morgante, Michele, and Bertrand, Benoit

Published
2020
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4. Differential associations between nucleotide polymorphisms and physiological traits in Norway spruce (Picea abiesKarst.) plants under contrasting water regimes

Author

Hrivnák, Matúš, primary, Krajmerová, Diana, additional, Kurjak, Daniel, additional, Konôpková, Alena, additional, Magni, Federica, additional, Scaglione, Davide, additional, Ditmarová, Ľubica, additional, Jamnická, Gabriela, additional, Marešová, Jana, additional, and Gömöry, Dušan, additional

Published
2022
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6. Differential associations between nucleotide polymorphisms and physiological traits in Norway spruce (Picea abies Karst.) plants under contrasting water regimes.

Author

Hrivnák, Matúš, Krajmerová, Diana, Kurjak, Daniel, Konôpková, Alena, Magni, Federica, Scaglione, Davide, Ditmarová, Ľubica, Jamnická, Gabriela, Marešová, Jana, and Gömöry, Dušan

Subjects
SILVER fir, KARST, CHLOROPHYLL spectra, MONOTERPENES, NORWAY spruce, CLIMATE change
Abstract

Norway spruce is an ecologically and commercially important species, which currently suffers from climate change and is expected to decline because of heat and drought stress. A manipulative experiment with drought-stressed and well-watered (control) seedlings was established, comprising five populations of Norway spruce coming from a small territory but distributed along a steep elevational transect from 550 to 1280 m.a.s.l. Plants were phenotyped at physiological traits (content of phytohormones and monoterpenes, chlorophyll a fluorescence, gas exchange and hyperspectral indices) and genotyped using ddRAD sequencing. After filtering, 34 127 polymorphisms (SNPs) were retained and used for analysis. Association tests revealed 42 SNP-variable pairs located across 29 scaffolds exhibiting significant associations, among them 20 were found for drought-stressed seedlings and 22 for control (watered) plants. However, there was no consistency between drought-stressed and control plants, no SNP-trait pair was common for both treatments. The study demonstrated that the identified genotype–phenotype associations can only be interpreted in the context of environmental setup preceding the assessment of phenotypic traits. [ABSTRACT FROM AUTHOR]

Published
2022
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7. Disentangling the Association of Hydroxychloroquine Treatment with Mortality in Covid-19 Hospitalized Patients through Hierarchical Clustering

Author

Di Castelnuovo, Augusto, primary, Gialluisi, Alessandro, additional, Antinori, Andrea, additional, Berselli, Nausicaa, additional, Blandi, Lorenzo, additional, Bonaccio, Marialaura, additional, Bruno, Raffaele, additional, Cauda, Roberto, additional, Costanzo, Simona, additional, Guaraldi, Giovanni, additional, Menicanti, Lorenzo, additional, Mennuni, Marco, additional, My, Ilaria, additional, Parruti, Giustino, additional, Patti, Giuseppe, additional, Perlini, Stefano, additional, Santilli, Francesca, additional, Signorelli, Carlo, additional, Stefanini, Giulio, additional, Vergori, Alessandra, additional, Ageno, Walter, additional, Agodi, Antonella, additional, Agostoni, Piergiuseppe, additional, Aiello, Luca, additional, Al Moghazi, Samir, additional, Arboretti, Rosa, additional, Aucella, Filippo, additional, Barbieri, Greta, additional, Barchitta, Martina, additional, Bonfanti, Paolo, additional, Cacciatore, Francesco, additional, Caiano, Lucia, additional, Cannata, Francesco, additional, Carrozzi, Laura, additional, Cascio, Antonio, additional, Castiglione, Giacomo, additional, Ciccullo, Arturo, additional, Cingolani, Antonella, additional, Cipollone, Francesco, additional, Colomba, Claudia, additional, Colombo, Crizia, additional, Crisetti, Annalisa, additional, Crosta, Francesca, additional, Danzi, Gian Battista, additional, D'Ardes, Damiano, additional, de Gaetano Donati, Katleen, additional, Di Gennaro, Francesco, additional, Di Tano, Giuseppe, additional, D'Offizi, Gianpiero, additional, Fusco, Francesco Maria, additional, Gaudiosi, Carlo, additional, Gentile, Ivan, additional, Gianfagna1, Francesco, additional, Giuliano, Gabriele, additional, Graziani, Emauele, additional, Guarnieri, Gabriella, additional, Langella, Valerio, additional, Larizza, Giovanni, additional, Leone, Armando, additional, Maccagni, Gloria, additional, Magni, Federica, additional, Maitan, Stefano, additional, Mancarella, Sandro, additional, Manuele, Rosa, additional, Mapelli, Massimo, additional, Maragna, Riccardo, additional, Marcucci, Rossella, additional, Maresca, Giulio, additional, Marongiu, Silvia, additional, Marotta, Claudia, additional, Marra, Lorenzo, additional, Mastroianni, Franco, additional, Mengozzi, Alessandro, additional, Meschiari, Marianna, additional, Milic, Jovana, additional, Minutolo, Filippo, additional, Mussinelli, Roberta, additional, Mussini, Cristina, additional, Musso, Maria, additional, Odone, Anna, additional, Olivieri, Marco, additional, Palimodde, Antonella, additional, Pasi, Emanuela, additional, Pesavento, Raffaele, additional, Petri, Francesco, additional, Pivato, Carlo A, additional, Poletti, Venerino, additional, Ravaglia, Claudia, additional, Righetti, Giulia, additional, Rognoni, Andrea, additional, Rossato, Marco, additional, Rossi, Ilaria, additional, Rossi, Marianna, additional, Sabena, Anna, additional, Salinaro, Francesco, additional, Sangiovanni, Vincenzo, additional, Sanrocco, Carlo, additional, Schiano Moriello, Nicola, additional, Scorzolini, Laura, additional, Sgariglia, Raffaella, additional, Simeone, Paola Giustina, additional, Spinicci, Michele, additional, Tamburrini, Enrica, additional, Torti, Carlo, additional, Trecarichi, Enrico Maria, additional, Vettor, Roberto, additional, Vianello, Andrea, additional, Vinceti, Marco, additional, Virdis, Agostino, additional, De Caterina, Raffaele, additional, and Iacoviello, Licia, additional

Published
2021
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8. Disentangling the Association of Hydroxychloroquine Treatment with Mortality in Covid-19 Hospitalized Patients through Hierarchical Clustering

Author

Di Castelnuovo, A, Gialluisi, A, Antinori, A, Berselli, N, Blandi, L, Bonaccio, M, Bruno, R, Cauda, R, Costanzo, S, Guaraldi, G, Menicanti, L, Mennuni, M, My, I, Parruti, G, Patti, G, Perlini, S, Santilli, F, Signorelli, C, Stefanini, G, Vergori, A, Ageno, W, Agodi, A, Agostoni, P, Aiello, L, Al Moghazi, S, Arboretti, R, Aucella, F, Barbieri, G, Barchitta, M, Bonfanti, P, Cacciatore, F, Caiano, L, Cannata, F, Carrozzi, L, Cascio, A, Castiglione, G, Cicullo, A, Cingolani, A, Cipollone, F, Colomba, C, Colombo, C, Crisetti, A, Crosta, F, Danzi, G, D'Ardes, D, de Gaetano Donati, K, Di Gennaro, F, Di Tano, G, D'Offizi, G, Fusco, F, Gaudiosi, C, Gentile, I, Gianfagna1, F, Giuliano, G, Graziani, E, Guarnieri, G, Langella, V, Larizza, G, Leone, A, Maccagni, G, Magni, F, Maitan, S, Mancarella, S, Manuele, R, Mapelli, M, Maragna, R, Marcucci, R, Maresca, G, Marongiu, S, Marotta, C, Marra, L, Mastroianni, F, Mengozzi, A, Meschiari, M, Milic, J, Minutolo, F, Mussinelli, R, Mussini, C, Musso, M, Odone, A, Olivieri, M, Palimodde, A, Pasi, E, Pesavento, R, Petri, F, Pivato, C, Poletti, V, Ravaglia, C, Righetti, G, Rognoni, A, Rossato, M, Rossi, I, Rossi, M, Sabena, A, Salinaro, F, Sangiovanni, V, Sanrocco, C, Schiano Moriello, N, Scorzolini, L, Sgariglia, R, Simeone, P, Spinicci, M, Tamburrini, E, Torti, C, Trecarichi, E, Vettor, R, Vianello, A, Vinceti, M, Virdis, A, De Caterina, R, Iacoviello, L, Di Castelnuovo, Augusto, Gialluisi, Alessandro, Antinori, Andrea, Berselli, Nausicaa, Blandi, Lorenzo, Bonaccio, Marialaura, Bruno, Raffaele, Cauda, Roberto, Costanzo, Simona, Guaraldi, Giovanni, Menicanti, Lorenzo, Mennuni, Marco, My, Ilaria, Parruti, Giustino, Patti, Giuseppe, Perlini, Stefano, Santilli, Francesca, Signorelli, Carlo, Stefanini, Giulio, Vergori, Alessandra, Ageno, Walter, Agodi, Antonella, Agostoni, Piergiuseppe, Aiello, Luca, Al Moghazi, Samir, Arboretti, Rosa, Aucella, Filippo, Barbieri, Greta, Barchitta, Martina, Bonfanti, Paolo, Cacciatore, Francesco, Caiano, Lucia, Cannata, Francesco, Carrozzi, Laura, Cascio, Antonio, Castiglione, Giacomo, Cicullo, Arturo, Cingolani, Antonella, Cipollone, Francesco, Colomba, Claudia, Colombo, Crizia, Crisetti, Annalisa, Crosta, Francesca, Danzi, Gian Battista, D'Ardes, Damiano, de Gaetano Donati, Katleen, Di Gennaro, Francesco, Di Tano, Giuseppe, D'Offizi, Gianpiero, Fusco, Francesco Maria, Gaudiosi, Carlo, Gentile, Ivan, Gianfagna1, Francesco, Giuliano, Gabriele, Graziani, Emauele, Guarnieri, Gabriella, Langella, Valerio, Larizza, Giovanni, Leone, Armando, Maccagni, Gloria, Magni, Federica, Maitan, Stefano, Mancarella, Sandro, Manuele, Rosa, Mapelli, Massimo, Maragna, Riccardo, Marcucci, Rossella, Maresca, Giulio, Marongiu, Silvia, Marotta, Claudia, Marra, Lorenzo, Mastroianni, Franco, Mengozzi, Alessandro, Meschiari, Marianna, Milic, Jovana, Minutolo, Filippo, Mussinelli, Roberta, Mussini, Cristina, Musso, Maria, Odone, Anna, Olivieri, Marco, Palimodde, Antonella, Pasi, Emanuela, Pesavento, Raffaele, Petri, Francesco, Pivato, Carlo A, Poletti, Venerino, Ravaglia, Claudia, Righetti, Giulia, Rognoni, Andrea, Rossato, Marco, Rossi, Ilaria, Rossi, Marianna, Sabena, Anna, Salinaro, Francesco, Sangiovanni, Vincenzo, Sanrocco, Carlo, Schiano Moriello, Nicola, Scorzolini, Laura, Sgariglia, Raffaella, Simeone, Paola Giustina, Spinicci, Michele, Tamburrini, Enrica, Torti, Carlo, Trecarichi, Enrico Maria, Vettor, Roberto, Vianello, Andrea, Vinceti, Marco, Virdis, Agostino, De Caterina, Raffaele, Iacoviello, Licia, Di Castelnuovo, A, Gialluisi, A, Antinori, A, Berselli, N, Blandi, L, Bonaccio, M, Bruno, R, Cauda, R, Costanzo, S, Guaraldi, G, Menicanti, L, Mennuni, M, My, I, Parruti, G, Patti, G, Perlini, S, Santilli, F, Signorelli, C, Stefanini, G, Vergori, A, Ageno, W, Agodi, A, Agostoni, P, Aiello, L, Al Moghazi, S, Arboretti, R, Aucella, F, Barbieri, G, Barchitta, M, Bonfanti, P, Cacciatore, F, Caiano, L, Cannata, F, Carrozzi, L, Cascio, A, Castiglione, G, Cicullo, A, Cingolani, A, Cipollone, F, Colomba, C, Colombo, C, Crisetti, A, Crosta, F, Danzi, G, D'Ardes, D, de Gaetano Donati, K, Di Gennaro, F, Di Tano, G, D'Offizi, G, Fusco, F, Gaudiosi, C, Gentile, I, Gianfagna1, F, Giuliano, G, Graziani, E, Guarnieri, G, Langella, V, Larizza, G, Leone, A, Maccagni, G, Magni, F, Maitan, S, Mancarella, S, Manuele, R, Mapelli, M, Maragna, R, Marcucci, R, Maresca, G, Marongiu, S, Marotta, C, Marra, L, Mastroianni, F, Mengozzi, A, Meschiari, M, Milic, J, Minutolo, F, Mussinelli, R, Mussini, C, Musso, M, Odone, A, Olivieri, M, Palimodde, A, Pasi, E, Pesavento, R, Petri, F, Pivato, C, Poletti, V, Ravaglia, C, Righetti, G, Rognoni, A, Rossato, M, Rossi, I, Rossi, M, Sabena, A, Salinaro, F, Sangiovanni, V, Sanrocco, C, Schiano Moriello, N, Scorzolini, L, Sgariglia, R, Simeone, P, Spinicci, M, Tamburrini, E, Torti, C, Trecarichi, E, Vettor, R, Vianello, A, Vinceti, M, Virdis, A, De Caterina, R, Iacoviello, L, Di Castelnuovo, Augusto, Gialluisi, Alessandro, Antinori, Andrea, Berselli, Nausicaa, Blandi, Lorenzo, Bonaccio, Marialaura, Bruno, Raffaele, Cauda, Roberto, Costanzo, Simona, Guaraldi, Giovanni, Menicanti, Lorenzo, Mennuni, Marco, My, Ilaria, Parruti, Giustino, Patti, Giuseppe, Perlini, Stefano, Santilli, Francesca, Signorelli, Carlo, Stefanini, Giulio, Vergori, Alessandra, Ageno, Walter, Agodi, Antonella, Agostoni, Piergiuseppe, Aiello, Luca, Al Moghazi, Samir, Arboretti, Rosa, Aucella, Filippo, Barbieri, Greta, Barchitta, Martina, Bonfanti, Paolo, Cacciatore, Francesco, Caiano, Lucia, Cannata, Francesco, Carrozzi, Laura, Cascio, Antonio, Castiglione, Giacomo, Cicullo, Arturo, Cingolani, Antonella, Cipollone, Francesco, Colomba, Claudia, Colombo, Crizia, Crisetti, Annalisa, Crosta, Francesca, Danzi, Gian Battista, D'Ardes, Damiano, de Gaetano Donati, Katleen, Di Gennaro, Francesco, Di Tano, Giuseppe, D'Offizi, Gianpiero, Fusco, Francesco Maria, Gaudiosi, Carlo, Gentile, Ivan, Gianfagna1, Francesco, Giuliano, Gabriele, Graziani, Emauele, Guarnieri, Gabriella, Langella, Valerio, Larizza, Giovanni, Leone, Armando, Maccagni, Gloria, Magni, Federica, Maitan, Stefano, Mancarella, Sandro, Manuele, Rosa, Mapelli, Massimo, Maragna, Riccardo, Marcucci, Rossella, Maresca, Giulio, Marongiu, Silvia, Marotta, Claudia, Marra, Lorenzo, Mastroianni, Franco, Mengozzi, Alessandro, Meschiari, Marianna, Milic, Jovana, Minutolo, Filippo, Mussinelli, Roberta, Mussini, Cristina, Musso, Maria, Odone, Anna, Olivieri, Marco, Palimodde, Antonella, Pasi, Emanuela, Pesavento, Raffaele, Petri, Francesco, Pivato, Carlo A, Poletti, Venerino, Ravaglia, Claudia, Righetti, Giulia, Rognoni, Andrea, Rossato, Marco, Rossi, Ilaria, Rossi, Marianna, Sabena, Anna, Salinaro, Francesco, Sangiovanni, Vincenzo, Sanrocco, Carlo, Schiano Moriello, Nicola, Scorzolini, Laura, Sgariglia, Raffaella, Simeone, Paola Giustina, Spinicci, Michele, Tamburrini, Enrica, Torti, Carlo, Trecarichi, Enrico Maria, Vettor, Roberto, Vianello, Andrea, Vinceti, Marco, Virdis, Agostino, De Caterina, Raffaele, and Iacoviello, Licia

Abstract

The efficacy of hydroxychloroquine (HCQ) in treating SARS-CoV-2 infection is harshly debated, with observational and experimental studies reporting contrasting results. To clarify the role of HCQ in Covid-19 patients, we carried out a retrospective observational study of 4,396 unselected patients hospitalized for Covid-19 in Italy (February–May 2020). Patients’ characteristics were collected at entry, including age, sex, obesity, smoking status, blood parameters, history of diabetes, cancer, cardiovascular and chronic pulmonary diseases, and medications in use. These were used to identify subtypes of patients with similar characteristics through hierarchical clustering based on Gower distance. Using multivariable Cox regressions, these clusters were then tested for association with mortality and modification of effect by treatment with HCQ. We identified two clusters, one of 3,913 younger patients with lower circulating inflammation levels and better renal function, and one of 483 generally older and more comorbid subjects, more prevalently men and smokers. The latter group was at increased death risk adjusted by HCQ (HR[CI95%] = 3.80[3.08-4.67]), while HCQ showed an independent inverse association (0.51[0.43-0.61]), as well as a significant influence of cluster∗HCQ interaction (). This was driven by a differential association of HCQ with mortality between the high (0.89[0.65-1.22]) and the low risk cluster (0.46[0.39-0.54]). These effects survived adjustments for additional medications in use and were concordant with associations with disease severity and outcome. These findings suggest a particularly beneficial effect of HCQ within low risk Covid-19 patients and may contribute to clarifying the current controversy on HCQ efficacy in Covid-19 treatment.

Published
2021

9. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for extremely low genetic variation in wild and cultivated germplasm

Author

Scalabrin, Simone, Toniutti, Lucile, Di Gaspero, Gabriele, Scaglione, Davide, Magris, Gabriele, Vidotto, Michele, Pinosio, Sara, Cattonaro, Frederica, Magni, Federica, Jurman, Irena, Cerutti, Mario, Suggi Liverani, Furio, Navarini, Luciano, Del Terra, Lorenzo, Pellegrino, Gloria, Ruosi, Manuela Rosanna, Vitulo, Nicola, Valle, Giorgio, Pallavicini, Alberto, Graziosi, Giorgio, Klein, Patricia E., Bentley, Nolan, Murray, Seth C., Solano, William, Al Hakimi, Amin, Schilling, Timothy, Montagnon, Christophe, Kotch, George, Bertrand, Benoît, Morgante, Michele, Scalabrin, Simone, Toniutti, Lucile, Di Gaspero, Gabriele, Scaglione, Davide, Magris, Gabriele, Vidotto, Michele, Pinosio, Sara, Cattonaro, Frederica, Magni, Federica, Jurman, Irena, Cerutti, Mario, Suggi Liverani, Furio, Navarini, Luciano, Del Terra, Lorenzo, Pellegrino, Gloria, Ruosi, Manuela Rosanna, Vitulo, Nicola, Valle, Giorgio, Pallavicini, Alberto, Graziosi, Giorgio, Klein, Patricia E., Bentley, Nolan, Murray, Seth C., Solano, William, Al Hakimi, Amin, Schilling, Timothy, Montagnon, Christophe, Kotch, George, Bertrand, Benoît, and Morgante, Michele

Abstract

RATIONALE - The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. METHODS - We studied an individual of C. arabica 'Bourbon Vermelho'. A BAC library of 175,872 BAC clones was constructed and sequenced using an Illumina HiSeq2000. Each BAC pool was assembled independently with the tool ABySS and scaffolded with SSPACE. Genotyping by sequencing (GBS) was conducted using the restriction enzyme PstI followed by single-end sequencing on an Illumina HiSeq2000. SNP calling was performed using Stacks. Principal Component Analysis was performed using the R package ade4. A hierarchical study of the diversity has been conducted using a model-based clustering procedure with admixture as implemented in STRUCTURE. RESULTS - We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugenioides subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. CONCLUSIONS & PERSPECTIVES - We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distrib

Published
2021

12. Features of the organization of bread wheat chromosome 5BS based on physical mapping

Author

Salina, Elena A., primary, Nesterov, Mikhail A., additional, Frenkel, Zeev, additional, Kiseleva, Antonina A., additional, Timonova, Ekaterina M., additional, Magni, Federica, additional, Vrána, Jan, additional, Šafář, Jan, additional, Šimková, Hana, additional, Doležel, Jaroslav, additional, Korol, Abraham, additional, and Sergeeva, Ekaterina M., additional

Published
2018
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13. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

Author

Barabaschi, Delfina, primary, Magni, Federica, additional, Volante, Andrea, additional, Gadaleta, Agata, additional, Šimková, Hana, additional, Scalabrin, Simone, additional, Prazzoli, Maria Lucia, additional, Bagnaresi, Paolo, additional, Lacrima, Katia, additional, Michelotti, Vania, additional, Desiderio, Francesca, additional, Orrù, Luigi, additional, Mazzamurro, Valentina, additional, Fricano, Agostino, additional, Mastrangelo, AnnaMaria, additional, Tononi, Paola, additional, Vitulo, Nicola, additional, Jurman, Irena, additional, Frenkel, Zeev, additional, Cattonaro, Federica, additional, Morgante, Michele, additional, Blanco, Antonio, additional, Doležel, Jaroslav, additional, Delledonne, Massimo, additional, Stanca, Antonio M., additional, Cattivelli, Luigi, additional, and Valè, Giampiero, additional

Published
2015
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14. Molecular diversity and landscape genomics of the crop wild relative <italic>Triticum urartu</italic> across the Fertile Crescent.

Author

Brunazzi, Alice, Scaglione, Davide, Talini, Rebecca Fiorella, Miculan, Mara, Magni, Federica, Poland, Jesse, Enrico Pè, Mario, Brandolini, Andrea, and Dell'Acqua, Matteo

Subjects
WHEAT genetics, WHEAT breeding, LANDSCAPE ecology, PLANT chromosomes, PHYTOGEOGRAPHY
Abstract

Summary: Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next‐generation sequencing was used to generate 1.3 million genome‐wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the Au subgenome of modern wheat. A set of 75 511 high‐quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R2 = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the Au subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome‐wide association approach, identifying several marker–environment associations (MEAs). Fifty‐seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding. [ABSTRACT FROM AUTHOR]

Published
2018
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16. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

Author

Raats, Dina, Frenkel, Zeev, Krugman, Tamar, Dodek, Itay, Sela, Hanan, Šimková, Hana, Magni, Federica, Cattonaro, Federica, Vautrin, Sonia, Bergès, Hélène, Wicker, Thomas, Keller, Beat, Leroy, Philippe, Philippe, Romain, Paux, Etienne, Doležel, Jaroslav, Feuillet, Catherine, Korol, Abraham, Fahima, Tzion, Raats, Dina, Frenkel, Zeev, Krugman, Tamar, Dodek, Itay, Sela, Hanan, Šimková, Hana, Magni, Federica, Cattonaro, Federica, Vautrin, Sonia, Bergès, Hélène, Wicker, Thomas, Keller, Beat, Leroy, Philippe, Philippe, Romain, Paux, Etienne, Doležel, Jaroslav, Feuillet, Catherine, Korol, Abraham, and Fahima, Tzion

Abstract

BACKGROUND: The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. RESULTS: Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. Chromosome 1BS gene space spans the entire length of the chromosome arm, with 76% of the genes organized in small gene-islands, accompanied by a two fold increase in gene density from the centromere to the telomere. CONCLUSIONS: This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes, and a non-uniform size expansion along the centromere-telomere axis, compared with other model cereal genomes. The high quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

Published
2013

17. A physical map of the short arm of wheat chromosome 1A

Author

Breen, James, Wicker, Thomas, Shatalina, Margarita, Frenkel, Zeev, Bertin, Isabelle, Philippe, Romain, Spielmeyer, Wolfgang, Šimková, Hana, Šafář, Jan, Cattonaro, Federica, Scalabrin, Simone, Magni, Federica, Vautrin, Sonia, Bergès, Hélène, Paux, Etienne, Fahima, Tzion, Doležel, Jaroslav, Korol, Abraham, Feuillet, Catherine, Keller, Beat, Breen, James, Wicker, Thomas, Shatalina, Margarita, Frenkel, Zeev, Bertin, Isabelle, Philippe, Romain, Spielmeyer, Wolfgang, Šimková, Hana, Šafář, Jan, Cattonaro, Federica, Scalabrin, Simone, Magni, Federica, Vautrin, Sonia, Bergès, Hélène, Paux, Etienne, Fahima, Tzion, Doležel, Jaroslav, Korol, Abraham, Feuillet, Catherine, and Keller, Beat

Abstract

Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.

Published
2013

18. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

Author

Philippe, Romain, primary, Paux, Etienne, additional, Bertin, Isabelle, additional, Sourdille, Pierre, additional, Choulet, Fréderic, additional, Laugier, Christel, additional, Šimková, Hana, additional, Šafář, Jan, additional, Bellec, Arnaud, additional, Vautrin, Sonia, additional, Frenkel, Zeev, additional, Cattonaro, Federica, additional, Magni, Federica, additional, Scalabrin, Simone, additional, Martis, Mihaela M, additional, Mayer, Klaus FX, additional, Korol, Abraham, additional, Bergès, Hélène, additional, Doležel, Jaroslav, additional, and Feuillet, Catherine, additional

Published
2013
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19. Physical Mapping Integrated with Syntenic Analysis to Characterize the Gene Space of the Long Arm of Wheat Chromosome 1A

Author

Lucas, Stuart J., primary, Akpınar, Bala Anı, additional, Kantar, Melda, additional, Weinstein, Zohar, additional, Aydınoğlu, Fatma, additional, Šafář, Jan, additional, Šimková, Hana, additional, Frenkel, Zeev, additional, Korol, Abraham, additional, Magni, Federica, additional, Cattonaro, Federica, additional, Vautrin, Sonia, additional, Bellec, Arnaud, additional, Bergès, Hélène, additional, Doležel, Jaroslav, additional, and Budak, Hikmet, additional

Published
2013
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21. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Author

Sara Pinosio, Gloria Pellegrino, Lucile Toniutti, Gabriele Magris, Timothy Schilling, Gabriele Di Gaspero, Benoît Bertrand, Seth C. Murray, Simone Scalabrin, Davide Scaglione, Amin Al Hakimi, Irena Jurman, Giorgio Graziosi, Nicola Vitulo, Giorgio Valle, Frederica Cattonaro, Michele Morgante, Manuela Rosanna Ruosi, Patricia E. Klein, Mario Cerutti, Luciano Navarini, Alberto Pallavicini, Lorenzo Del Terra, Furio Suggi Liverani, Nolan Bentley, Michele Vidotto, Christophe Montagnon, Federica Magni, William Solano, Scalabrin, Simone, Toniutti, Lucile, Di Gaspero, Gabriele, Scaglione, Davide, Magris, Gabriele, Vidotto, Michele, Pinosio, Sara, Cattonaro, Federica, Magni, Federica, Jurman, Irena, Cerutti, Mario, Suggi Liverani, Furio, Navarini, Luciano, Del Terra, Lorenzo, Pellegrino, Gloria, Ruosi, Manuela Rosanna, Vitulo, Nicola, Valle, Giorgio, Pallavicini, Alberto, Graziosi, Giorgio, Klein, Patricia E, Bentley, Nolan, Murray, Seth, Solano, William, Al Hakimi, Amin, Schilling, Timothy, Montagnon, Christophe, Morgante, Michele, and Bertrand, Benoit

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Yemen, Computational biology and bioinformatics, Evolution, Genetics, Plant sciences, Genomics, Coffea arabica, lcsh:Medicine, Coffea, 01 natural sciences, F30 - Génétique et amélioration des plantes, Genome Size, Dynamique des populations, lcsh:Science, Computational biology and bioinformatic, 2. Zero hunger, Multidisciplinary, Coffea arabica , genome sequencing, plants, biology, U10 - Informatique, mathématiques et statistiques, plants, Polyploïdie, Center of origin, genome sequencing, Plant science, Genome, Plant, Costa Rica, Crops, Agricultural, xxxx, Canephora, Introgression, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Bioinformatique, Genetic, Genetic variation, Genome size, Genetic diversity, Whole Genome Sequencing, lcsh:R, biology.organism_classification, Tetraploidy, 030104 developmental biology, Evolutionary biology, Genomic, lcsh:Q, 010606 plant biology & botany
Abstract

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Published
2020

22. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution.

Author

Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Doležel J, Feuillet C, Korol A, and Fahima T

Subjects
Chromosomes, Artificial, Bacterial, Chromosomes, Plant classification, Evolution, Molecular, Gene Order, Genes, Plant, Genomics methods, Chromosomes, Plant genetics, Physical Chromosome Mapping methods, Triticum genetics
Abstract

Background: The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution., Results: Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere., Conclusions: This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

Published
2013
Full Text
View/download PDF

23. A physical map of the short arm of wheat chromosome 1A.

Author

Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Simková H, Safář J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Bergès H, Paux E, Fahima T, Doležel J, Korol A, Feuillet C, and Keller B

Subjects
Chromosomes, Artificial, Bacterial, Genetic Markers, Multigene Family, Nucleic Acid Hybridization, Polymerase Chain Reaction, Chromosome Mapping, Chromosomes, Plant
Abstract

Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.

Published
2013
Full Text
View/download PDF

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