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1. De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

Author

Venturini Luca, Ferrarini Alberto, Zenoni Sara, Tornielli Giovanni Battista, Fasoli Marianna, Santo Silvia Dal, Minio Andrea, Buson Genny, Tononi Paola, Zago Elisa Debora, Zamperin Gianpiero, Bellin Diana, Pezzotti Mario, and Delledonne Massimo

Subjects
Transcriptomics, RNA-Seq, de novo assembly, Grape, Varietal diversity, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors. Results We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome. Conclusions The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.

Published
2013
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2. Multiple wheat genomes reveal global variation in modern breeding

Author

Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T, Brinton, Jemima, Ramirez-Gonzalez, Ricardo H, Kolodziej, Markus C, Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Fritz, Allen K, Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A, Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C, Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J, Sharpe, Andrew G, Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G, Handa, Hirokazu, Shimizu, Kentaro K, Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus FX, Poland, Jesse, Stein, Nils, McCartney, Curt A, Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J

Subjects
Genetics, Biotechnology, Human Genome, Acclimatization, Animals, Centromere, Chromosome Mapping, Cloning, Molecular, DNA Copy Number Variations, DNA Transposable Elements, Edible Grain, Genes, Plant, Genetic Introgression, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Insecta, Internationality, NLR Proteins, Plant Breeding, Plant Diseases, Plant Proteins, Polymorphism, Single Nucleotide, Polyploidy, Triticum, General Science & Technology
Abstract

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Published
2020

3. Scaling associative classification for very large datasets

Author

Venturini, Luca, Baralis, Elena, and Garza, Paolo

Subjects
Computer Science - Learning, Computer Science - Artificial Intelligence, Computer Science - Distributed, Parallel, and Cluster Computing, Statistics - Machine Learning
Abstract

Supervised learning algorithms are nowadays successfully scaling up to datasets that are very large in volume, leveraging the potential of in-memory cluster-computing Big Data frameworks. Still, massive datasets with a number of large-domain categorical features are a difficult challenge for any classifier. Most off-the-shelf solutions cannot cope with this problem. In this work we introduce DAC, a Distributed Associative Classifier. DAC exploits ensemble learning to distribute the training of an associative classifier among parallel workers and improve the final quality of the model. Furthermore, it adopts several novel techniques to reach high scalability without sacrificing quality, among which a preventive pruning of classification rules in the extraction phase based on Gini impurity. We ran experiments on Apache Spark, on a real large-scale dataset with more than 4 billion records and 800 million distinct categories. The results showed that DAC improves on a state-of-the-art solution in both prediction quality and execution time. Since the generated model is human-readable, it can not only classify new records, but also allow understanding both the logic behind the prediction and the properties of the model, becoming a useful aid for decision makers.

Published
2018
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4. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution

Author

Barchi, Lorenzo, Pietrella, Marco, Venturini, Luca, Minio, Andrea, Toppino, Laura, Acquadro, Alberto, Andolfo, Giuseppe, Aprea, Giuseppe, Avanzato, Carla, Bassolino, Laura, Comino, Cinzia, Molin, Alessandra Dal, Ferrarini, Alberto, Maor, Louise Chappell, Portis, Ezio, Reyes-Chin-Wo, Sebastian, Rinaldi, Riccardo, Sala, Tea, Scaglione, Davide, Sonawane, Prashant, Tononi, Paola, Almekias-Siegl, Efrat, Zago, Elisa, Ercolano, Maria Raffaella, Aharoni, Asaph, Delledonne, Massimo, Giuliano, Giovanni, Lanteri, Sergio, and Rotino, Giuseppe Leonardo

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Horticultural Production, Biotechnology, Human Genome, Chromosomes, Plant, Ethylenes, Evolution, Molecular, Gene Regulatory Networks, Genome, Plant, MicroRNAs, Solanum melongena
Abstract

With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.

Published
2019

5. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Author

Clavijo, Bernardo J, Venturini, Luca, Schudoma, Christian, Accinelli, Gonzalo Garcia, Kaithakottil, Gemy, Wright, Jonathan, Borrill, Philippa, Kettleborough, George, Heavens, Darren, Chapman, Helen, Lipscombe, James, Barker, Tom, Lu, Fu-Hao, McKenzie, Neil, Raats, Dina, Ramirez-Gonzalez, Ricardo H, Coince, Aurore, Peel, Ned, Percival-Alwyn, Lawrence, Duncan, Owen, Trösch, Josua, Yu, Guotai, Bolser, Dan M, Namaati, Guy, Kerhornou, Arnaud, Spannagl, Manuel, Gundlach, Heidrun, Haberer, Georg, Davey, Robert P, Fosker, Christine, Di Palma, Federica, Phillips, Andrew L, Millar, A Harvey, Kersey, Paul J, Uauy, Cristobal, Krasileva, Ksenia V, Swarbreck, David, Bevan, Michael W, and Clark, Matthew D

Subjects
Genetics, Biotechnology, Human Genome, Algorithms, Contig Mapping, Genome, Plant, Molecular Sequence Annotation, Plant Proteins, Polymorphism, Genetic, Polyploidy, Translocation, Genetic, Triticum, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Published
2017

6. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Author

Scott, Michael F., Ladejobi, Olufunmilayo, Amer, Samer, Bentley, Alison R., Biernaskie, Jay, Boden, Scott A., Clark, Matt, Dell’Acqua, Matteo, Dixon, Laura E., Filippi, Carla V., Fradgley, Nick, Gardner, Keith A., Mackay, Ian J., O’Sullivan, Donal, Percival-Alwyn, Lawrence, Roorkiwal, Manish, Singh, Rakesh Kumar, Thudi, Mahendar, Varshney, Rajeev Kumar, Venturini, Luca, Whan, Alex, Cockram, James, and Mott, Richard

Published
2020
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7. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

Author

Bellucci, Elisa, Bitocchi, Elena, Ferrarini, Alberto, Benazzo, Andrea, Biagetti, Eleonora, Klie, Sebastian, Minio, Andrea, Rau, Domenico, Rodriguez, Monica, Panziera, Alex, Venturini, Luca, Attene, Giovanna, Albertini, Emidio, Jackson, Scott A., Nanni, Laura, Fernie, Alisdair R., Nikoloski, Zoran, Bertorelle, Giorgio, Delledonne, Massimo, and Papa, Roberto

Published
2014

12. Multiple wheat genomes reveal global variation in modern breeding

Author

70983196, 10273492, Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T., Brinton, Jemima, Ramirez-Gonzalez, Ricardo H., Kolodziej, Markus C., Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Fritz, Allen K., Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A., Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C., Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J., Sharpe, Andrew G., Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G., Handa, Hirokazu, Shimizu, Kentaro K., Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus F. X., Poland, Jesse, Stein, Nils, McCartney, Curt A., Spannagl, Manuel, Wicker, Thomas, Pozniak, Curtis J., 70983196, 10273492, Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T., Brinton, Jemima, Ramirez-Gonzalez, Ricardo H., Kolodziej, Markus C., Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Fritz, Allen K., Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A., Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C., Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J., Sharpe, Andrew G., Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G., Handa, Hirokazu, Shimizu, Kentaro K., Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus F. X., Poland, Jesse, Stein, Nils, McCartney, Curt A., Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J.

Abstract

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome, and the lack of genome-assembly data for multiple wheat lines. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Published
2020

14. Shifting the limits in wheat research and breeding using a fully annotated reference genome

Author

Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, Wang, Le, Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, and Wang, Le

Abstract

Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.

Published
2018

15. Efficient and accurate detection of splice junctions from RNAseq with Portcullis

Author

Mapleson, Daniel, Venturini, Luca, Kaithakottil, Gemy, and Swarbreck, David

Subjects
Alternative splicing, splice, Computational biology, Data mining, Biology, Threading (protein sequence), computer.software_genre, Genome, computer, DNA sequencing, Gene transcript
Abstract

Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed, however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Herein we describe the extent of this problem using popular RNA-seq mapping tools, and present a new method, called Portcullis, to rapidly filter false SJs junctions from spliced alignments produced by any RNA-seq mapper capable of creating SAM/BAM files. We show that Portcullis distinguishes between genuine and false positive junctions to a high-degree of accuracy across different species, samples, expression levels, error profiles and read lengths. Portcullis makes efficient use of memory and threading and, to our knowledge, is currently the only SJ prediction tool that reliably scales for use with large RNAseq datasets and large highly fragmented genomes, whilst delivering highly accurate SJs.AvailabilityPortcullis is available under the GPLv3 license at: http://maplesond.github.io/portcullis/Contactdaniel.mapleson@earlham.ac.uk

Published
2017
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19. Progress on Exploitation and Dissemination Plans-Part II

Author

Lopez, Miguel, Quirós, José, Ocón, José, Monjas, Miguel, Ordogoizti, Bruno, Zhu, Bo, Gómez, Sandra, Vararuv, Stanislav, Mozo, Alberto, Apiletti, Daniele, Baralis, Elena, Cerquitelli, Tania, Chiusano, Silvia, Garza, Paolo, Pulvirenti, Fabio, Venturini, Luca, Anastasiou, Stefanos, Owezarski, Philippe, Arias, Fernando, Owezarski, Philippe, SATEC (SATEC), Ericsson Spain (ERC), Universidad Politécnica de Madrid (UPM), Politecnico di Torino = Polytechnic of Turin (Polito), ADAPTIT, Centre National de la Recherche Scientifique (CNRS), SATEC, Ericsson Spain, Universidad politécnica de Madrid, Politecnico di Torino, LAAS-CNRS, and EMC

Subjects
[INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], [INFO.INFO-NI] Computer Science [cs]/Networking and Internet Architecture [cs.NI]
Published
2016

21. Exploitation and Dissemination Plans

Author

Mozo, Alberto, Ordozgoiti, Bruno, Fernández, Enrique, Gomez, Sandra, Martínez, Alex, Mara, Alex, Zhu, Bo, Vakaruv, Stanislav, Apiletti, Daniele, Baralis, Elena, Venturini, Luca, Chiusano, Silvia, Garza, Paolo, Cerquitelli, Tania, Grimaudo, Luigi, Anastasiou, Stefanos, López, Miguel, Owezarski, Philippe, Arias, Fernando, Universidad Politécnica de Madrid (UPM), Centre National de la Recherche Scientifique (CNRS), Universidad Politécnica de Madrid (Universidad Politécnica de Madrid), Politecnico di Torino, ADAPTIT, SATEC, CNRS-LAAS, EMC, and Owezarski, Philippe

Subjects
[INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], [INFO.INFO-NI] Computer Science [cs]/Networking and Internet Architecture [cs.NI]
Published
2015

22. UAV, profili giuridici

Author

Venturini, Luca

Subjects
Unmanned aerial vehicle, Profili giuridici, Settore IUS/06 - Diritto Della Navigazione
Published
2013

24. DE NOVO RECONSTRUCTION OF THE VITIS VINIFERA CV. CORVINA TRANSCRIPTOME

Author

Venturini, Luca, Ferrarini, Alberto, Noel, D., Tononi, P., Buson, G., Zenoni, Sara, Bellin, Diana, Pezzotti, Mario, and Delledonne, Massimo

Subjects
De novo assembly, gene expression profiling, Vitis vinifera cv. Corvina, transcriptome, next-generation sequencing
Published
2011

26. Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway

Author

Degu, Asfaw, primary, Hochberg, Uri, additional, Sikron, Noga, additional, Venturini, Luca, additional, Buson, Genny, additional, Ghan, Ryan, additional, Plaschkes, Inbar, additional, Batushansky, Albert, additional, Chalifa-Caspi, Vered, additional, Mattivi, Fulvio, additional, Delledonne, Massimo, additional, Pezzotti, Mario, additional, Rachmilevitch, Shimon, additional, Cramer, Grant R, additional, and Fait, Aaron, additional

Published
2014
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28. De novotranscriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

Author

Venturini, Luca, primary, Ferrarini, Alberto, additional, Zenoni, Sara, additional, Tornielli, Giovanni Battista, additional, Fasoli, Marianna, additional, Santo, Silvia Dal, additional, Minio, Andrea, additional, Buson, Genny, additional, Tononi, Paola, additional, Zago, Elisa Debora, additional, Zamperin, Gianpiero, additional, Bellin, Diana, additional, Pezzotti, Mario, additional, and Delledonne, Massimo, additional

Published
2013
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30. TP53 Alterations Including Missense Mutations, Aberrant Exon-Junctions and Internal Intron Retentions Are Frequent and May Contribute to MDM2 Antagonist-Resistance in B-Acute Lymphoblastic leukemia

Author

Iacobucci, Ilaria, primary, Ferrari, Anna, additional, Trino, Stefania, additional, Lonetti, Annalisa, additional, Papayannidis, Cristina, additional, Ferrarini, Alberto, additional, Venturini, Luca, additional, Abbenante, Maria Chiara, additional, Parisi, Sarah, additional, Cattina, Federica, additional, Soverini, Simona, additional, Paolini, Stefania, additional, Russo, Domenico, additional, Vignetti, Marco, additional, Pane, Fabrizio, additional, Musto, Pellegrino, additional, Delledonne, Massimo, additional, Baccarani, Michele, additional, and Martinelli, Giovanni, additional

Published
2011
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31. High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome.

Author

Silva, Cecilia Da, Zamperin, Gianpiero, Ferrarini, Alberto, Minio, Andrea, Molin, Alessandra Dal, Venturini, Luca, Buson, Genny, Tononi, Paola, Avanzato, Carla, Zago, Elisa, Boido, Eduardo, Dellacassa, Eduardo, Gaggero, Carina, Pezzotti, Mario, Carrau, Francisco, and Delledonne, Massimo

Subjects
BERRIES, GRAPES, GENOMES, GENES, VITIS vinifera, RNA sequencing, PHENOTYPES, RED wines
Abstract

The grapevine (Vitis vinifera) cultivar Tannat is cultivated mainly in Uruguay for the production of high-quality red wines. Tannat berries have unusually high levels of polyphenolic compounds, producing wines with an intense purple color and remarkable antioxidant properties. We investigated the genetic basis of these important characteristics by sequencing the genome of the Uruguayan Tannat clone UY11 using Illumina technology, followed by a mixture of de novo assembly and iterative mapping onto the PN40024 reference genome. RNA sequencing data for genome reannotation were processed using a combination of reference-guided annotation and de novo transcript assembly, allowing 5901 previously unannotated or unassembled genes to be defined and resulting in the discovery of 1873 genes that were not shared with PN40024. Expression analysis showed that these cultivar-specific genes contributed substantially (up to 81.24%) to the overall expression of enzymes involved in the synthesis of phenolic and polyphenolic compounds that contribute to the unique characteristics of the Tannat berries. The characterization of the Tannat genome therefore indicated that the grapevine reference genome lacks many genes that appear to be relevant for the varietal phenotype. [ABSTRACT FROM AUTHOR]

Published
2013
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32. Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program.

Author

Fasoli, Marianna, Santo, Silvia Dal, Zenoni, Sara, Tornielli, Giovanni Battista, Farina, Lorenzo, Zamboni, Anita, Porceddu, Andrea, Venturini, Luca, Bicego, Manuele, Murino, Vittorio, Ferrarini, Alberto, Delledonne, Massimo, and Pezzotti, Mario

Subjects
GENETIC regulation, WOODY plants, TRANSCRIPTOMES, DEVELOPMENTAL programs, GRAPES, BIOMARKERS, VITIS vinifera
Abstract

We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed ∼91% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants. [ABSTRACT FROM AUTHOR]

Published
2012
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33. Gemello digitale di un ponte in muratura mediante analisi modale operazionale e algoritmi genetici

Author

Venturini, Luca, thesis supervisor: Marzani, Alessandro, Venturini, Luca, and thesis supervisor: Marzani, Alessandro

Abstract

Il monitoraggio strutturale è un processo che, nell’ambito ingegneristico, mira a identificare la nascita e/o l’evoluzione del danno nelle strutture. Il paradigma prevede l’installazione di sensori sulla struttura, per monitorarne nel tempo alcuni parametri, e l’utilizzo di modelli strutturali e algoritmi che a partire dai dati misurati siano in grado di rilevarne eventuali danni. In seno al monitoraggio strutturale vive il problema di identificazione strutturale, cioè l’insieme di strategie analitiche e sperimentali atte a calibrare i modelli strutturali, quindi a generare dei gemelli digitali delle strutture. Queste strategie si basano sull'estrazione di caratteristiche dai dati misurati, con tecniche di identificazione quali la Analisi Modale Sperimentale (EMA) e l’Analisi Modale Operazionale (OMA), e di schemi di ottimizzazione euristici che operano allo scopo di “aggiornare” i modelli strutturali. La tesi si è focalizzata sulla generazione di un gemello digitale, ai fini del monitoraggio strutturale, di un ponte ferroviario multi-campata in muratura, sulla linea ferroviaria Foggia-Napoli. Attraverso l’analisi statica e dinamica, condotte su due modelli a elementi finiti (FEM) realizzati con i software Abaqus e SAP2000, è stato possibile calcolare dati quali le frequenze naturali e le deformate modali (caratteristiche del ponte iniziale). Si è poi proceduto a definire possibili scenari di danno variando la rigidezza di alcune parti/porzioni del ponte, utilizzati poi per estrarre i dati dei ponti danneggiati (caratteristiche del ponte danneggiato). Attraverso uno schema agli algoritmi genetici, il modello iniziale è stato aggiornato generando il gemello digitale del ponte danneggiato. L’algoritmo genetico implementato sul software Matlab prevede un processo iterativo volto a minimizzare una funzione obiettivo basata sulla differenza tra le frequenze del ponte iniziale e quelle del ponte danneggiato, al variale di alcuni parametri fisici del modello.

34. Gemello digitale di un ponte in muratura mediante analisi modale operazionale e algoritmi genetici

Author

Venturini, Luca, thesis supervisor: Marzani, Alessandro, Venturini, Luca, and thesis supervisor: Marzani, Alessandro

Abstract

Il monitoraggio strutturale è un processo che, nell’ambito ingegneristico, mira a identificare la nascita e/o l’evoluzione del danno nelle strutture. Il paradigma prevede l’installazione di sensori sulla struttura, per monitorarne nel tempo alcuni parametri, e l’utilizzo di modelli strutturali e algoritmi che a partire dai dati misurati siano in grado di rilevarne eventuali danni. In seno al monitoraggio strutturale vive il problema di identificazione strutturale, cioè l’insieme di strategie analitiche e sperimentali atte a calibrare i modelli strutturali, quindi a generare dei gemelli digitali delle strutture. Queste strategie si basano sull'estrazione di caratteristiche dai dati misurati, con tecniche di identificazione quali la Analisi Modale Sperimentale (EMA) e l’Analisi Modale Operazionale (OMA), e di schemi di ottimizzazione euristici che operano allo scopo di “aggiornare” i modelli strutturali. La tesi si è focalizzata sulla generazione di un gemello digitale, ai fini del monitoraggio strutturale, di un ponte ferroviario multi-campata in muratura, sulla linea ferroviaria Foggia-Napoli. Attraverso l’analisi statica e dinamica, condotte su due modelli a elementi finiti (FEM) realizzati con i software Abaqus e SAP2000, è stato possibile calcolare dati quali le frequenze naturali e le deformate modali (caratteristiche del ponte iniziale). Si è poi proceduto a definire possibili scenari di danno variando la rigidezza di alcune parti/porzioni del ponte, utilizzati poi per estrarre i dati dei ponti danneggiati (caratteristiche del ponte danneggiato). Attraverso uno schema agli algoritmi genetici, il modello iniziale è stato aggiornato generando il gemello digitale del ponte danneggiato. L’algoritmo genetico implementato sul software Matlab prevede un processo iterativo volto a minimizzare una funzione obiettivo basata sulla differenza tra le frequenze del ponte iniziale e quelle del ponte danneggiato, al variale di alcuni parametri fisici del modello.

35. TP53Alterations Including Missense Mutations, Aberrant Exon-Junctions and Internal Intron Retentions Are Frequent and May Contribute to MDM2 Antagonist-Resistance in B-Acute Lymphoblastic leukemia

Author

Iacobucci, Ilaria, Ferrari, Anna, Trino, Stefania, Lonetti, Annalisa, Papayannidis, Cristina, Ferrarini, Alberto, Venturini, Luca, Abbenante, Maria Chiara, Parisi, Sarah, Cattina, Federica, Soverini, Simona, Paolini, Stefania, Russo, Domenico, Vignetti, Marco, Pane, Fabrizio, Musto, Pellegrino, Delledonne, Massimo, Baccarani, Michele, and Martinelli, Giovanni

Abstract

Abstract 1484

Published
2011
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36. A Planning and Control System for Self-Driving Racing Vehicles

Author

Adriano Fagiolini, Francesco Amerotti, Federico Massa, Alessandro Settimi, Stefano De Caro, Andrea Biondo, Andrea Corti, Lucia Pallottino, Danio Caporale, Luca Venturini, Caporale, Danilo, Fagiolini, Adriano, Pallottino, Lucia, Settimi, Alessandro, Biondo, Andrea, Amerotti, Francesco, Massa, Federico, De Caro, Stefano, Corti, Andrea, and Venturini, Luca

Subjects
Operations research, Renewable Energy, Sustainability and the Environment, Computer science, Control (management), Energy Engineering and Power Technology, Computer Science Applications1707 Computer Vision and Pattern Recognition, Autonomous robots, self-driving vehicles, racing, robotics challenge, Pedestrian, Industrial and Manufacturing Engineering, Competition (economics), self-driving vehicles, Autonomous robot, racing, Computer Networks and Communication, Settore ING-INF/04 - Automatica, Artificial Intelligence, Autonomous robots, Control system, self-driving vehicle, Trajectory, Key (cryptography), Robot, robotics challenge, Everyday life, Instrumentation
Abstract

Autonomous robots will soon enter our everyday life as self-driving cars. These vehicles are designed to behave according to certain sets of cooperative rules, such as traffic ones, and to respond to events that might be unpredictable in their occurrence but predictable in their nature, such as a pedestrian suddenly crossing a street, or another car losing control. As civilian autonomous cars will cross the road, racing autonomous cars are under development, which will require superior Artificial Intelligence Drivers to perform in structured but uncertain conditions. We describe some preliminary results obtained during the development of a planning and control system as key elements of an Artificial Intelligence driver for the competition scenario.

Published
2018
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