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2. A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm

Author

Scalabrin, Simone, Magris, Gabriele, Liva, Mario, Vitulo, Nicola, Vidotto, Michele, Scaglione, Davide, Del Terra, Lorenzo, Ruosi, Manuela Rosanna, Navarini, Luciano, Pellegrino, Gloria, Berny Mier y Teran, Jorge Carlos, Toniutti, Lucile, Suggi Liverani, Furio, Cerutti, Mario, Di Gaspero, Gabriele, and Morgante, Michele

Published
2024
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6. Lignocellulolytic Potential of Microbial Consortia Isolated from a Local Biogas Plant: The Case of Thermostable Xylanases Secreted by Mesophilic Bacteria

Author

Bombardi, Luca, primary, Salini, Andrea, additional, Aulitto, Martina, additional, Zuliani, Luca, additional, Andreolli, Marco, additional, Bordoli, Paola, additional, Coltro, Annalaura, additional, Vitulo, Nicola, additional, Zaccone, Claudio, additional, Lampis, Silvia, additional, and Fusco, Salvatore, additional

Published
2024
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7. CK2β Regulates Hematopoietic Stem Cell Biology and Erythropoiesis

Author

Quotti Tubi, Laura, primary, Canovas Nunes, Sara, additional, Mandato, Elisa, additional, Pizzi, Marco, additional, Vitulo, Nicola, additional, D’Agnolo, Mirco, additional, Colombatti, Raffaella, additional, Martella, Maddalena, additional, Boaro, Maria Paola, additional, Doriguzzi Breatta, Elena, additional, Fregnani, Anna, additional, Spinello, Zaira, additional, Nabergoj, Mitja, additional, Filhol, Odile, additional, Boldyreff, Brigitte, additional, Albiero, Mattia, additional, Fadini, Gian Paolo, additional, Gurrieri, Carmela, additional, Vianello, Fabrizio, additional, Semenzato, Gianpietro, additional, Manni, Sabrina, additional, Trentin, Livio, additional, and Piazza, Francesco, additional

Published
2023
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10. 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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11. Supplementary data for An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype

Author

Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille, Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, and Rustenholz, Camille

Published
2023

12. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype

Author

Federal Ministry of Food and Agriculture (Germany), European Commission, Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille, Federal Ministry of Food and Agriculture (Germany), European Commission, Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, and Rustenholz, Camille

Abstract

The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from 9 selfings of cv. "Helfensteiner" (cross of cv. "Pinot noir" and "Schiava grossa") instead of a single "Pinot noir". These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing toward the eventual elaboration of the grapevine pangenome.

Published
2023

16. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype

Author

Velt, Amandine, primary, Frommer, Bianca, additional, Blanc, Sophie, additional, Holtgräwe, Daniela, additional, Duchêne, Éric, additional, Dumas, Vincent, additional, Grimplet, Jérôme, additional, Hugueney, Philippe, additional, Kim, Catherine, additional, Lahaye, Marie, additional, Matus, José Tomás, additional, Navarro-Payá, David, additional, Orduña, Luis, additional, Tello-Ruiz, Marcela K, additional, Vitulo, Nicola, additional, Ware, Doreen, additional, and Rustenholz, Camille, additional

Published
2023
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17. CK2β-regulated signaling controls B cell differentiation and function

Author

Quotti Tubi, Laura, primary, Mandato, Elisa, additional, Canovas Nunes, Sara, additional, Arjomand, Arash, additional, Zaffino, Fortunato, additional, Manni, Sabrina, additional, Casellato, Alessandro, additional, Macaccaro, Paolo, additional, Vitulo, Nicola, additional, Zumerle, Sara, additional, Filhol, Odile, additional, Boldyreff, Brigitte, additional, Siebel, Christian W., additional, Viola, Antonella, additional, Valle, Giorgio, additional, Mainoldi, Federica, additional, Casola, Stefano, additional, Cancila, Valeria, additional, Gulino, Alessandro, additional, Tripodo, Claudio, additional, Pizzi, Marco, additional, Dei Tos, Angelo Paolo, additional, Trentin, Livio, additional, Semenzato, Gianpietro, additional, and Piazza, Francesco, additional

Published
2023
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23. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish

Author

Pauletto, Marianna, Manousaki, Tereza, Ferraresso, Serena, Babbucci, Massimiliano, Tsakogiannis, Alexandros, Louro, Bruno, Vitulo, Nicola, Quoc, Viet Ha, Carraro, Roberta, Bertotto, Daniela, Franch, Rafaella, Maroso, Francesco, Aslam, Muhammad L., Sonesson, Anna K., Simionati, Barbara, Malacrida, Giorgio, Cestaro, Alessandro, Caberlotto, Stefano, Sarropoulou, Elena, Mylonas, Costantinos C., Power, Deborah M., Patarnello, Tomaso, Canario, Adelino V. M., Tsigenopoulos, Costas, and Bargelloni, Luca

Published
2018
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25. Randomized Double-Blind Crossover Study for Evaluating a Probiotic Mixture on Gastrointestinal and Behavioral Symptoms of Autistic Children

Author

Guidetti, Cristina, primary, Salvini, Elena, additional, Viri, Maurizio, additional, Deidda, Francesca, additional, Amoruso, Angela, additional, Visciglia, Annalisa, additional, Drago, Lorenzo, additional, Calgaro, Matteo, additional, Vitulo, Nicola, additional, Pane, Marco, additional, and Caucino, Anna Claudia, additional

Published
2022
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27. An improved reference of the PN40024 grapevine genome assembly (PN40024.v4) and annotations

Author

Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille, Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K., Vitulo, Nicola, Ware, Doreen, and Rustenholz, Camille

Published
2022

28. Salivary microbiota composition may discriminate between patients with eosinophilic oesophagitis ( EoE ) and non‐EoE subjects

Author

Facchin, Sonia, primary, Calgaro, Matteo, additional, Pandolfo, Mattia, additional, Caldart, Federico, additional, Ghisa, Matteo, additional, Greco, Eliana, additional, Sattin, Eleonora, additional, Valle, Giorgio, additional, Dellon, Evan S., additional, Vitulo, Nicola, additional, and Savarino, Edoardo Vincenzo, additional

Published
2022
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32. red wine intervention does not modify plasma trimethylamine N-oxide but is associated with broad shifts in the plasma metabolome and gut microbiota composition.

Author

Haas, Elisa A, Saad, Mario J A, Santos, Andrey, Vitulo, Nicola, Lemos, Wilson J F, Martins, Aline M A, Picossi, Carolina R C, Favarato, Desidério, Gaspar, Renato S, Magro, Daniéla O, Libby, Peter, Laurindo, Francisco R M, Da Luz, Protasio L, and Study, for the WineFlora

Subjects
HIGH throughput screening (Drug development), MEN'S health, HIGH performance liquid chromatography, OENOTHERAPY, GUT microbiome, METABOLOMICS, TIME, RNA, HEALTH outcome assessment, AMINES, RANDOMIZED controlled trials, CORONARY artery disease, DESCRIPTIVE statistics, STATISTICAL sampling, CROSSOVER trials, OXIDATION-reduction reaction
Abstract

Background Gut microbiota profiles are closely related to cardiovascular diseases through mechanisms that include the reported deleterious effects of metabolites, such as trimethylamine N -oxide (TMAO), which have been studied as diagnostic and therapeutic targets. Moderate red wine (RW) consumption is reportedly cardioprotective, possibly by affecting the gut microbiota. Objectives To investigate the effects of RW consumption on the gut microbiota, plasma TMAO, and the plasma metabolome in men with documented coronary artery disease (CAD) using a multiomics assessment in a crossover trial. Methods We conducted a randomized, crossover, controlled trial involving 42 men (average age, 60 y) with documented CAD comparing 3-wk RW consumption (250 mL/d, 5 d/wk) with an equal period of alcohol abstention, both preceded by a 2-wk washout period. The gut microbiota was analyzed via 16S rRNA high-throughput sequencing. Plasma TMAO was evaluated by LC-MS/MS. The plasma metabolome of 20 randomly selected participants was evaluated by ultra-high-performance LC-MS/MS. The effect of RW consumption was assessed by individual comparisons using paired tests during the abstention and RW periods. Results Plasma TMAO did not differ between RW intervention and alcohol abstention, and TMAO concentrations showed low intraindividual concordance over time, with an intraclass correlation coefficient of 0.049 during the control period. After RW consumption, there was significant remodeling of the gut microbiota, with a difference in β diversity and predominance of Parasutterella, Ruminococcaceae , several Bacteroides species, and Prevotella. Plasma metabolomic analysis revealed significant changes in metabolites after RW consumption, consistent with improved redox homeostasis. Conclusions Modulation of the gut microbiota may contribute to the putative cardiovascular benefits of moderate RW consumption. The low intraindividual concordance of TMAO presents challenges regarding its role as a cardiovascular risk biomarker at the individual level. This study was registered at clinical trials.gov as NCT03232099. [ABSTRACT FROM AUTHOR]

Published
2022
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33. Comparative analysis identifies micro-RNA associated with nutrient homeostasis, development and stress response in Arabidopsis thaliana upon high Zn and metal hyperaccumulator Arabidopsis helleri

Author

Fasani, Elisa, DalCorso, Giovanni, Zorzi, Gianluca, Vitulo, Nicola, and Furini, Antonella

Subjects
Arabidopsis halleri, Zn homeostasis, Arabidopsis thaliana, Arabidopsis Proteins, Ecophysiology, Stress and Adaptation, Arabidopsis, Nutrients, Plant, stress, Zinc, MicroRNAs, nutrition, Gene Expression Regulation, Gene Expression Regulation, Plant, Homeostasis, development, metal hyperaccumulation, miRNA
Abstract

miRNAs have been found to be key players in mineral homeostasis, both in the control of nutrient balance and in the response to toxic trace elements. However, the effect of Zn excess on miRNAs has not been elucidated; moreover, no data are present regarding miRNAs in hyperaccumulator species, where metal homeostasis is tightly regulated. Therefore, expression levels of mature miRNAs were measured by RNA‐Seq in Zn‐sensitive Arabidopsis thaliana grown in control conditions and upon high Zn, in soil and in Zn‐hyperaccumulator Arabidopsis halleri grown in control conditions. Differential expression of notable miRNAs and their targets was confirmed by real‐time RT‐PCR. The comparison in A. thaliana revealed a small subset modulated upon Zn treatment that is associated with stress response and nutrient homeostasis. On the other hand, a more consistent group of miRNAs was differentially expressed in A. halleri compared with A. thaliana, reflecting inherent differences in nutritional requirements and response to stresses and plant growth and development. Overall, these results confirm the involvement of miRNAs in Zn homeostasis and support the hypothesis of distinct regulatory pathways in hyperaccumulator species.

Published
2021

34. 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

37. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure

Author

Lauro, Federico M., Tran, Khiem, Vezzi, Alessandro, Vitulo, Nicola, Valle, Giorgio, and Bartlett, Douglas H.

Subjects
Gram-negative bacteria -- Physiological aspects, Gram-negative bacteria -- Genetic aspects, Transposons -- Properties, Transposons -- Influence, Mutagenesis -- Research, Quantitative trait loci -- Properties, Quantitative trait loci -- Influence, Bacterial growth -- Genetic aspects, Biological sciences
Abstract

Microorganisms adapted to piezopsychrophilic growth dominate the majority of the biosphere that is at relatively constant low temperatures and high pressures, but the genetic bases for the adaptations are largely unknown. Here we report the use of transposon mutagenesis with the deep-sea bacterium Photobacterium profundum strain SS9 to isolate dozens of mutant strains whose growth is impaired at low temperature and/or whose growth is altered as a function of hydrostatic pressure. In many cases the gene mutation-growth phenotype relationship was verified by complementation analysis. The largest fraction of loci associated with temperature sensitivity were involved in the biosynthesis of the cell envelope, in particular the biosynthesis of extracellular polysaccharide. The largest fraction of loci associated with pressure sensitivity were involved in chromosomal structure and function. Genes for ribosome assembly and function were found to be important for both low-temperature and high-pressure growth. Likewise, both adaptation to temperature and adaptation to pressure were affected by mutations in a number of sensory and regulatory loci, suggesting the importance of signal transduction mechanisms in adaptation to either physical parameter. These analyses were the first global analyses of genes conditionally required for low-temperature or high-pressure growth in a deep-sea microorganism.

Published
2008

38. Assessment of single cell RNA-seq statistical methods on microbiome data

Author

Calgaro, Matteo, Romualdi, Chiara, Waldron, Levi, Risso, Davide, and Vitulo, Nicola

Abstract

The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has shown that commonly used methods do not control the false discovery rate due to the peculiarity of these data (e.g. high sparsity), leading to an abundance of false positive results. Since single-cell RNA-seq shares some of these peculiarities, we apply methods developed for single cell differential expression to microbiome data. We compare these approaches to methods developed for bulk RNA-seq and microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, consistency, replicability, and power. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing. A simulation framework is developed to assess the impact of experimental design in power analysis. Our analyses suggest that DESeq2 and limma-voom show the best performance. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner.

Published
2020
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41. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla: the French-Italian public consortium for grapevine genome characterization

Author

Jaillon, Olivier, Aury, Jean-Marc, Noel, Benjamin, Policriti, Alberto, Clepet, Christian, Casagrande, Alberto, Choisne, Nathalie, Aubourg, Sebastien, Vitulo, Nicola, Jubin, Claire, Vezzi, Alessandro, Legeai, Fabrice, Hugueney, Philippe, Dasilva, Corinne, Horner, David, Mica, Erica, Jublot, Delphine, Poulain, Julie, Bruyere, Clemence, Billault, Alain, Segurens, Beatrice, Gouyvenoux, Michel, Ugarte, Edgardo, Cattonaro, Federica, Anthouard, Veronique, Vico, Virginie, Del Fabbro, Cristian, Alaux, Michael, Gaspero, Gabriele Di, Dumas, Vincent, Felice, Nicoletta, Paillard, Sophie, Juman, Irena, Moroldo, Marco, Scalabrin, Simone, Canaguier, Aurelie, Clainche, Isabelle Le, Malacrida, Giorgio, Durand, Eleonore, Pesole, Graziano, Laucou, Valerie, Chatelet, Philippe, Merdinoglu, Didier, Delledonne, Massimo, Pezzotti, Mario, Lecharny, Alain, Scarpelli, Claude, Artiguenave, Francois, Pe, M. Enrico, Valle, Giorgio, Morgante, Michele, Caboche, Michel, Adam-Blondon, Anne-Francoise, Weissenbach, Jean, Quetier, Francis, and Wincker, Patrick

Subjects
Grapes -- Genetic aspects, Genomes -- Identification and classification -- Genetic aspects, Angiosperms -- Natural history -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Identification and classification, Genetic aspects, Natural history
Abstract

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics [...]

Published
2007

46. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile

Author

Vitulo Nicola, Vezzi Alessandro, Romualdi Chiara, Campanaro Stefano, and Valle Giorgio

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In this work we propose an improved phylogenetic profile analysis on 14 Vibrionaceae genomes, to study the evolution of this family on the basis of gene content. The phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently present or absent within different genomes. This allows the prediction of hypothetical functions on the basis of a shared phylogenetic profiles. Moreover this approach is useful to identify putative laterally transferred elements on the basis of their presence on distantly phylogenetically related bacteria. Results Vibrionaceae ORFs were aligned against all the available bacterial proteomes. Phylogenetic profile is defined as an array of distances, based on aminoacid substitution matrixes, from single genes to all their orthologues. Final phylogenetic profiles, derived from non-redundant list of all ORFs, was defined as the median of all the profiles belonging to the cluster. The resulting phylogenetic profiles matrix contains gene clusters on the rows and organisms on the columns. Cluster analysis identified groups of "core genes" with a widespread high similarity across all the organisms and several clusters that contain genes homologous only to a limited set of organisms. On each of these clusters, COG class enrichment has been calculated. The analysis reveals that clusters of core genes have the highest number of enriched classes, while the others are enriched just for few of them like DNA replication, recombination and repair. Conclusion We found that mobile elements have heterogeneous profiles not only across the entire set of organisms, but also within Vibrionaceae; this confirms their great influence on bacteria evolution even inside the same family. Furthermore, several hypothetical proteins highly correlate with mobile elements profiles suggesting a possible horizontal transfer mechanism for the evolution of these genes. Finally, we suggested the putative role of some ORFs having an unknown function on the basis of their phylogenetic profile similarity to well characterized genes.

Published
2007
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47. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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49. A draft genome of sweet cherry ( Prunus avium L.) reveals genome‐wide and local effects of domestication

Author

Pinosio, Sara, primary, Marroni, Fabio, additional, Zuccolo, Andrea, additional, Vitulo, Nicola, additional, Mariette, Stephanie, additional, Sonnante, Gabriella, additional, Aravanopoulos, Filippos A., additional, Ganopoulos, Ioannis, additional, Palasciano, Marino, additional, Vidotto, Michele, additional, Magris, Gabriele, additional, Iezzoni, Amy, additional, Vendramin, Giovanni G., additional, and Morgante, Michele, additional

Published
2020
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50. Engineering a 3D in vitro model of human skeletal muscle at the single fiber scale

Author

Urciuolo, Anna, primary, Serena, Elena, additional, Ghua, Rusha, additional, Zatti, Susi, additional, Giomo, Monica, additional, Mattei, Nicolò, additional, Vetralla, Massimo, additional, Selmin, Giulia, additional, Luni, Camilla, additional, Vitulo, Nicola, additional, Valle, Giorgio, additional, Vitiello, Libero, additional, and Elvassore, Nicola, additional

Published
2020
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