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1. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Published
2024
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2. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Author

Ranawaka, Buddhini, An, Jiyuan, Lorenc, Michał T., Jung, Hyungtaek, Sulli, Maria, Aprea, Giuseppe, Roden, Sally, Llaca, Victor, Hayashi, Satomi, Asadyar, Leila, LeBlanc, Zacharie, Ahmed, Zuba, Naim, Fatima, de Campos, Samanta Bolzan, Cooper, Tal, de Felippes, Felipe F., Dong, Pengfei, Zhong, Silin, Garcia-Carpintero, Victor, Orzaez, Diego, Dudley, Kevin J., Bombarely, Aureliano, Bally, Julia, Winefield, Christopher, Giuliano, Giovanni, and Waterhouse, Peter M.

Published
2023
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5. Author Correction: A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Author

Ranawaka, Buddhini, An, Jiyuan, Lorenc, Michał T., Jung, Hyungtaek, Sulli, Maria, Aprea, Giuseppe, Roden, Sally, Llaca, Victor, Hayashi, Satomi, Asadyar, Leila, LeBlanc, Zacharie, Ahmed, Zuba, Naim, Fatima, de Campos, Samanta Bolzan, Cooper, Tal, de Felippes, Felipe F., Dong, Pengfei, Zhong, Silin, Garcia-Carpintero, Victor, Orzaez, Diego, Dudley, Kevin J., Bombarely, Aureliano, Bally, Julia, Winefield, Christopher, Giuliano, Giovanni, and Waterhouse, Peter M.

Published
2024
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6. Safety and Preliminary Efficacy of Mesenchymal Stromal Cell (ORBCEL-M) Therapy in Diabetic Kidney Disease: A Randomized Clinical Trial (NEPHSTROM)

Author

Perico, Norberto, Remuzzi, Giuseppe, Griffin, Matthew D., Cockwell, Paul, Maxwell, Alexander P., Casiraghi, Federica, Rubis, Nadia, Peracchi, Tobia, Villa, Alessandro, Todeschini, Marta, Carrara, Fabiola, Magee, Bernadette A., Ruggenenti, Piero L., Rota, Stefano, Cappelletti, Laura, McInerney, Veronica, Griffin, Tomás P., Islam, Md Nahidul, Introna, Martino, Pedrini, Olga, Golay, Josée, Finnerty, Andrew A., Smythe, Jon, Fibbe, Willem E., Elliman, Stephen J., OʼBrien, Timothy, Perico, Norberto, Remuzzi, Giuseppe, Griffin, Matthew D., Cockwell, Paul, Maxwell, Alexander P., Casiraghi, Federica, Rubis, Nadia, Peracchi, Tobia, Villa, Alessandro, Todeschini, Marta, Carrara, Fabiola, Magee, Bernadette A., Ruggenenti, Piero L., Rota, Stefano, Cappelletti, Laura, McInerney, Veronica, Griffin, Tomás P., Islam, Md Nahidul, Introna, Martino, Pedrini, Olga, Golay, Josée, Finnerty, Andrew A., Smythe, Jon, Fibbe, Willem E., Elliman, Stephen J., OʼBrien, Timothy, Portalupi, Valentina, Gotti, Eliana, Perticucci, Elena, Natali, Grazia, Rambaldi, Alessandro, Gritti, Giuseppe, Barbui, Anna Maria, Ferrari, Silvia, Mariani, Silvia, Borleri, Gianmaria, Hennessy, Michelle, Cormican, Sarah, Devaney, Nathan, Phan, Cassandra, Hanson, Amy, Martyn, Sara, Buckley, Joy, Naughton, Sean, Woods, Julie, Kelly, Caroline, Hayat, Amjad, Chanouzas, Dimitrios, Fifer, Lesley, Kuningas, Kulli, Walmsley-Allen, Natalie, Desai, Amisha, Atchinson, Lucy, White, Sinead, Suresh, Vijayan, Kirkham, Katie, Evans, Fiona, Little, Mark, Messa, Piergiorgio, Yap, Christina, Diadei, Olimpia, Boccardo, Paola, Noreiko, Oleksii, Martinetti, Davide, Giuliano, Giovanni Antonio, Perna, Annalisa, Cugini, Daniela, Ferrari, Silvia, Stucchi, Nadia, Mister, Marilena, OʼFlynn, Lisa, Shimizu, Yuka, Roelofs, Helene, Steeneveld, Esther, Wieles, Brigitte, Capelli, Chiara, Austen, Eric, Murray, Helen, Hanson, Vivien, Chan, Jenny, Duffy, Aoife, Holohan, Miriam, Krawczyk, Janusz, Duggan, Matthew, Connolly, Lauren, Hyatt, Amjad, Krawczyk, Janusz, Tarpey, Margaret, Naughton, Sean, Buckley, Joy, Asbagh, Layka Abbasi, Rice, Brent, Baila, Stefano, Davey, Grace, Creane, Michael, Clissmann, Ciaran, and Sweetnam, Mark

Published
2023
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8. On the Importance of Temporal Features in Domain Adaptation Methods for Action Recognition

Author

Conte, Donatello, Fioretti, Giuliano Giovanni, Sansone, Carlo, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Krzyzak, Adam, editor, Suen, Ching Y., editor, Torsello, Andrea, editor, and Nobile, Nicola, editor

Published
2022
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10. Global range expansion history of pepper ( Capsicum spp.) revealed by over 10,000 genebank accessions

Author

Tripodi, Pasquale, Rabanus-Wallace, Mark Timothy, Barchi, Lorenzo, Kale, Sandip, Esposito, Salvatore, Acquadro, Alberto, Schafleitner, Roland, van Zonneveld, Maarten, Prohens, Jaime, Diez, Maria José, Börner, Andreas, Salinier, Jérémy, Caromel, Bernard, Bovy, Arnaud, Boyaci, Filiz, Pasev, Gancho, Brandt, Ronny, Himmelbach, Axel, Portis, Ezio, Finkers, Richard, Lanteri, Sergio, Paran, Ilan, Lefebvre, Véronique, Giuliano, Giovanni, and Stein, Nils

Published
2021

11. Underwater optical communication systems

Author

Giuliano, Giovanni

Subjects
621.382, TA Engineering (General). Civil engineering (General)
Abstract

I present in this thesis the results of my research in the field of underwater optical communication system (UOCS). Recently, underwater free-space optical (FSO) communication has been one of the major interesting research subjects due to the high demand for underwater activities that require high-bandwidth and flexible solutions. An optical communication system consists of three main blocks: transmitter, medium and receiver. Therefore, I provide an introduction to the topic, outlining the physical reasons and the engineering challenges that are behind the following sections. Among others, the optical properties of ocean water, the optimum wavelength selection and a description of the main system components are provided so that the system link budget can be subsequently optimised. Various modulation schemes adopted in free-space optics communication are evaluated and compared with a focus on the most power-efficient modulation format that offers successful and reliable data transmission. The system performances are numerically investigated using statistical analysis techniques over a typical range of achievable SNR in an underwater scenario. The characterisation and the data performance of a commercial GaN-based laser diode operating at 450 nm are presented. The detrimental impact of the solar background power on the system performance and the strategy to minimise its contribution is also discussed for a conventional Silicon PIN detector and the novel Silicon PhotoMultiplier (SiPM) technology. The design trade-off between the performance improvement given by an optical narrow bandpass filter matching a Fraunhofer line and the field-of-view of the receiver is also presented. A flexible MATLAB model has been developed to simulate a range of different scenarios and evaluate the system performances in different situations and the necessary design trade-off. A novel free-space waveguiding method is also presented for laser-based underwater communication systems. The proposed Underwater Wireless Acousto-Optic Waveguide (UWAOW) generates a localised modification of the refractive index of seawater in response to an acoustic field. Two geometries and their modelling are provided in order to take advantage of the proposed technique. These results show the importance of this emerging, challenging and fascinating contemporary research field.

Published
2019
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12. Pepper variome reveals the history and key loci associated with fruit domestication and diversification

Author

Cao, Yacong, Zhang, Kang, Yu, Hailong, Chen, Shumin, Xu, Donghui, Zhao, Hong, Zhang, Zhenghai, Yang, Yinqing, Gu, Xiaozhen, Liu, Xinyan, Wang, Haiping, Jing, Yaxin, Mei, Yajie, Wang, Xiang, Lefebvre, Véronique, Zhang, Weili, Jin, Yuan, An, Dongliang, Wang, Risheng, Bosland, Paul, Li, Xixiang, Paran, Ilan, Zhang, Baoxi, Giuliano, Giovanni, Wang, Lihao, and Cheng, Feng

Published
2022
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13. 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

14. Fresh lemon juice supplementation for the prevention of recurrent stones in calcium oxalate nephrolithiasis: A pragmatic, prospective, randomised, open, blinded endpoint (PROBE) trial

Author

Ruggenenti, Piero, Caruso, Maria Rosa, Cortinovis, Monica, Perna, Annalisa, Peracchi, Tobia, Giuliano, Giovanni Antonio, Rota, Stefano, Brambilla, Paolo, Invernici, Giuliana, Villa, Davide, Diadei, Olimpia, Trillini, Matias, Natali, Grazia, and Remuzzi, Giuseppe

Published
2022
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15. Large-Scale Network-Based Observations of a Saharan Dust Event across the European Continent in Spring 2022.

Author

Papanikolaou, Christina-Anna, Papayannis, Alexandros, Gidarakou, Marilena, Abdullaev, Sabur F., Ajtai, Nicolae, Baars, Holger, Balis, Dimitris, Bortoli, Daniele, Bravo-Aranda, Juan Antonio, Collaud-Coen, Martine, de Rosa, Benedetto, Dionisi, Davide, Eleftheratos, Kostas, Engelmann, Ronny, Floutsi, Athena A., Abril-Gago, Jesús, Goloub, Philippe, Giuliano, Giovanni, Gumà-Claramunt, Pilar, and Hofer, Julian

Abstract

Between 14 March and 21 April 2022, an extensive investigation of an extraordinary Saharan dust intrusion over Europe was performed based on lidar measurements obtained by the European Aerosol Research Lidar Network (EARLINET). The dust episode was divided into two distinct periods, one in March and one in April, characterized by different dust transport paths. The dust aerosol layers were studied over 18 EARLINET stations, examining aerosol characteristics during March and April in four different regions (M-I, M-II, M-III, and M-IV and A-I, A-II, A-III, and A-IV, respectively), focusing on parameters such as aerosol layer thickness, center of mass (CoM), lidar ratio (LR), particle linear depolarization ratio (PLDR), and Ångström exponents (ÅE). In March, regions exhibited varying dust geometrical and optical properties, with mean CoM values ranging from approximately 3.5 to 4.8 km, and mean LR values typically between 36 and 54 sr. PLDR values indicated the presence of both pure and mixed dust aerosols, with values ranging from 0.20 to 0.32 at 355 nm and 0.24 to 0.31 at 532 nm. ÅE values suggested a range of particle sizes, with some regions showing a predominance of coarse particles. Aerosol Optical Depth (AOD) simulations from the NAAPS model indicated significant dust activity across Europe, with AOD values reaching up to 1.60. In April, dust aerosol layers were observed between 3.2 to 5.2 km. Mean LR values typically ranged from 35 to 51 sr at both 355 nm and 532 nm, while PLDR values confirmed the presence of dust aerosols, with mean values between 0.22 and 0.31 at 355 nm and 0.25 to 0.31 at 532 nm. The ÅE values suggested a mixture of particle sizes. The AOD values in April were generally lower, not exceeding 0.8, indicating a less intense dust presence compared to March. The findings highlight spatial and temporal variations in aerosol characteristics across the regions, during the distinctive periods. From 15 to 16 March 2022, Saharan dust significantly reduced UV-B radiation by approximately 14% over the ATZ station (Athens, GR). Backward air mass trajectories showed that the dust originated from the Western and Central Sahara when, during this specific case, the air mass trajectories passed over GRA (Granada, ES) and PAY (Payerne, CH) before reaching ATZ, maintaining high relative humidity and almost stable aerosol properties throughout its transport. Lidar data revealed elevated aerosol backscatter (baer) and PLDR values, combined with low LR and ÅE values, indicative of pure dust aerosols. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Solanum pennellii (LA5240) backcross inbred lines (BILs) for high resolution mapping in tomato.

Author

Torgeman, Shai, Pleban, Tzili, Goldberg, Yael, Ferrante, Paola, Aprea, Giuseppe, Giuliano, Giovanni, Yichie, Yoav, Fisher, Josef, Zemach, Itay, Koch, Amit, Rochsar, Edan, Oved, Matan, Bandel, Kfir, and Zamir, Dani

Subjects
SOLANUM, TOMATOES, PRUNING, TOMATO breeding, GENE families, CROP improvement
Abstract

SUMMARY: Wild species are an invaluable source of new traits for crop improvement. Over the years, the tomato community bred cultivated lines that carry introgressions from different species of the tomato tribe to facilitate trait discovery and mapping. The next phase in such projects is to find the genes that drive the identified phenotypes. This can be achieved by genotyping a few thousand individuals resulting in fine mapping that can potentially identify the causative gene. To couple trait discovery and fine mapping, we are presenting large, recombination‐rich, Backcross Inbred Line (BIL) populations involving an unexplored accession of the wild, green‐fruited species Solanum pennellii (LA5240; the 'Lost' Accession) with two modern tomato inbreds: LEA, determinate, and TOP, indeterminate. The LEA and TOP BILs are in BC2F6–8 generation and include 1400 and 500 lines, respectively. The BILs were genotyped with 5000 SPET markers, showing that in the euchromatic regions there was one recombinant every 17–18 Kb while in the heterochromatin a recombinant every 600–700 Kb (TOP and LEA respectively). To gain perspective on the topography of recombination we compared five independent members of the Self‐pruning gene family with their respective neighboring genes; based on PCR markers, in all cases we found recombinants. Further mapping analysis of two known morphological mutations that segregated in the BILs (self‐pruning and hairless) showed that the maximal delimited intervals were 73 Kb and 210 Kb, respectively, and included the known causative genes. The 'Lost'_BILs provide a solid framework to study traits derived from a drought‐tolerant wild tomato. Significance Statement: We are presenting a very large Introgression population from drought‐tolerant wild tomato species for fine mapping and epistasis analyses. [ABSTRACT FROM AUTHOR]

Published
2024
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17. A novel tomato inter-specific (Solanum lycopersicumvar.cerasiformeandS. pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

Author

Arrones, Andrea, primary, Antar, Oussama, additional, Pereira-Dias, Leandro, additional, Solana, Andrea, additional, Ferrante, Paola, additional, Aprea, Giuseppe, additional, Plazas, Mariola, additional, Prohens, Jaime, additional, Díez, María José, additional, Giuliano, Giovanni, additional, Gramazio, Pietro, additional, and Vilanova, Santiago, additional

Published
2024
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18. Exploring the Potential of Aeolus Lidar Mission for Ocean Color Applications

Author

Dionisi, Davide, primary, Bucci, Simone, additional, Cesarini, Claudia, additional, Colella, Simone, additional, D'Alimonte, Davide, additional, Di Ciolo, Lorenzo, additional, Di Girolamo, Paolo, additional, Di Paolantonio, Marco, additional, Franco, Noemi, additional, Gostinicchi, Giacomo, additional, Giuliano, Giovanni, additional, Kajiyama, Tamito, additional, Organelli, Emanuele, additional, Santoleri, Rosalia, additional, and Liberti, Gian Luigi, additional

Published
2024
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20. Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit.

Author

D'Esposito, Daniela, Ferriello, Francesca, Molin, Alessandra Dal, Diretto, Gianfranco, Sacco, Adriana, Minio, Andrea, Barone, Amalia, Di Monaco, Rossella, Cavella, Silvana, Tardella, Luca, Giuliano, Giovanni, Delledonne, Massimo, Frusciante, Luigi, and Ercolano, Maria Raffaella

Subjects
Cell Wall, Fruit, Transcription Factors, Systems Biology, Gene Expression Regulation, Plant, Genotype, Gene Dosage, Genome, Plant, Italy, Metabolome, Transcriptome, Food Quality, Solanum lycopersicum, Environment, Fruit quality, Network, Plasticity, Sensorial attributes, Genetics, Microbiology, Plant Biology, Crop and Pasture Production, Plant Biology & Botany
Abstract

BackgroundThe environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two "local" ones, San Marzano and Vesuviano in two different locations of Campania region (Italy).ResultsResponses to environment were more pronounced in the two "local" genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted.ConclusionsAlthough similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup.

Published
2017

22. Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency

Author

Desaint, Henri, primary, Hereil, Alexandre, additional, Belinchon-Moreno, Javier, additional, Carretero, Yolande, additional, Pelpoir, Esther, additional, Pascal, Michel, additional, Brault, Marie, additional, Dumont, Doriane, additional, Lecompte, François, additional, Laugier, Patricia, additional, Duboscq, Renaud, additional, Bitton, Frederique, additional, Grumic, Mara, additional, Giraud, Christophe, additional, Ferrante, Paola, additional, Giuliano, Giovanni, additional, Sunseri, Francesco, additional, and Causse, Mathilde, additional

Published
2023
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24. The genome and population genomics of allopolyploid Coffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Published
2024
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25. The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, primary, Rambani, Aditi, additional, Yu, Zhe, additional, Guyot, Romain, additional, Strickler, Susan, additional, Lepelley, Maud, additional, Wang, Cui, additional, Rajaraman, Sitaram, additional, Rastas, Pasi, additional, Zheng, Chunfang, additional, Muñoz, Daniella Santos, additional, Meidanis, João, additional, Paschoal, Alexandre Rossi, additional, Bawin, Yves, additional, Krabbenhoft, Trevor, additional, Wang, Zhen Qin, additional, Fleck, Steven, additional, Aussel, Rudy, additional, Bellanger, Laurence, additional, Charpagne, Aline, additional, Fournier, Coralie, additional, Kassam, Mohamed, additional, Lefebvre, Gregory, additional, Métairon, Sylviane, additional, Moine, Déborah, additional, Rigoreau, Michel, additional, Stolte, Jens, additional, Hamon, Perla, additional, Couturon, Emmanuel, additional, Tranchant-Dubreuil, Christine, additional, Mukherjee, Minakshi, additional, Lan, Tianying, additional, Engelhardt, Jan, additional, Stadler, Peter, additional, De Lemos, Samara Mireza Correia, additional, Suzuki, Suzana Ivamoto, additional, Sumirat, Ucu, additional, Man, Wai Ching, additional, Dauchot, Nicolas, additional, Orozco-Arias, Simon, additional, Garavito, Andrea, additional, Kiwuka, Catherine, additional, Musoli, Pascal, additional, Nalukenge, Anne, additional, Guichoux, Erwan, additional, Reinout, Havinga, additional, Smit, Martin, additional, Carretero-Paulet, Lorenzo, additional, Filho, Oliveiro Guerreiro, additional, Braghini, Masako Toma, additional, Padilha, Lilian, additional, Sera, Gustavo Hiroshi, additional, Ruttink, Tom, additional, Henry, Robert, additional, Marraccini, Pierre, additional, Van de Peer, Yves, additional, Andrade, Alan, additional, Domingues, Douglas, additional, Giuliano, Giovanni, additional, Mueller, Lukas, additional, Pereira, Luiz Filipe, additional, Plaisance, Stephane, additional, Poncet, Valerie, additional, Rombauts, Stephane, additional, Sankoff, David, additional, Albert, Victor A., additional, Crouzillat, Dominique, additional, de Kochko, Alexandre, additional, and Descombes, Patrick, additional

Published
2023
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26. Multi‐environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection

Author

McLeod, Louis, primary, Barchi, Lorenzo, additional, Tumino, Giorgio, additional, Tripodi, Pasquale, additional, Salinier, Jérémy, additional, Gros, Christophe, additional, Boyaci, Hatice Filiz, additional, Ozalp, Ramazan, additional, Borovsky, Yelena, additional, Schafleitner, Roland, additional, Barchenger, Derek, additional, Finkers, Richard, additional, Brouwer, Matthijs, additional, Stein, Nils, additional, Rabanus‐Wallace, Mark Timothy, additional, Giuliano, Giovanni, additional, Voorrips, Roeland, additional, Paran, Ilan, additional, and Lefebvre, Véronique, additional

Published
2023
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29. Moderate salt restriction with or without paricalcitol in type 2 diabetes and losartan-resistant macroalbuminuria (PROCEED): a randomised, double-blind, placebo-controlled, crossover trial

Author

Perico, Norberto, Ruggenenti, Piero, Remuzzi, Giuseppe, Rota, Stefano, Trillini, Matias, Ruggiero, Barbara, Aparicio, Maria Carolina, Prandini, Silvia, Cugini, Daniela, Gherardi, Giulia, Podestà, Manuel A, Trevisan, Roberto, Corsi, Anna, Bossi, Antonio C., Parvanova, Aneliya, Iliev, Ilian Petrov, Yakymchuk, S, Lecchi, Veruscka, Belviso, Antonio, Mangili, Ruggero, Rubis, Nadia, Calini, Wally, Diadei, Olimpia, Ene-Iordache, Bogdan, Carminati, Sergio, Martinetti, Davide, Giuliano, Giovanni Antonio, Perna, Annalisa, Peraro, Francesco, Russo, Angela, Gaspari, Flavio, Carrara, Fabiola, Ferrari, Silvia, Stucchi, Nadia, Cannata, Antonio Nicola, Boccardo, Paola, Peracchi, Sara, De Borst, Martin, Bettoni, Serena, Cattaneo, Irene, Franchina, Davide, Ha Phan, Haian, Igiraneza, Grace, Kaucsár, Tamas, Lima, Sergio Luis, Lunney, Meg, Tran, Huong, Abbate, Manuela, Bossi, Antonio C, and de Borst, Martin

Published
2018
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30. Co-expression of statistically over-represented peptides in proteomes: a key to phylogeny ?

Author

Ferraro, Luca, Giansanti, Andrea, Giuliano, Giovanni, and Rosato, Vittorio

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a phylogenetic distance is introduced and the corresponding distance matrix between proteomes is constructed. From the distance matrix a phylogenetic tree is inferred, following a standard procedure. It compares well with a reference tree deduced from a distance matrix obtained from the alignment of ribosomal RNA sequences. Our results are consistent with the hypothesis that biological evolution manifests itself with a modulation of basic correlations between shared peptides of short length, present in protein sequences. Moreover, the simple procedure we propose reconfirms that it is possible, sampling entire proteomes, to average the effects of lateral gene transfer and infer reasonable phylogenies., Comment: Minor typos corrected, partly rewritten conclusions and bibliography added

Published
2004

37. Conventional and new genetic resources for an eggplant breeding revolution.

Author

Gramazio, Pietro, Alonso, David, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Toppino, Laura, Barchi, Lorenzo, Portis, Ezio, Ferrante, Paola, Lanteri, Sergio, Rotino, Giuseppe Leonardo, Giuliano, Giovanni, Vilanova, Santiago, and Prohens, Jaime

Subjects
EGGPLANT, GERMPLASM, CLIMATE change adaptation, CLIMATE change, GENETIC variation
Abstract

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Production of Saffron Apocarotenoids in Nicotiana benthamiana Plants Genome-Edited to Accumulate Zeaxanthin Precursor

Author

Demurtas, Olivia Costantina, Sulli, Maria, Ferrante, Paola, Mini, Paola, Martí, Maricarmen, Aragonés, Verónica, Daròs, José-Antonio, and Giuliano, Giovanni

Abstract

Crocins are glycosylated apocarotenoids with strong coloring power and anti-oxidant, anticancer, and neuro-protective properties. We previously dissected the saffron crocin biosynthesis pathway, and demonstrated that the CsCCD2 enzyme, catalyzing the carotenoid cleavage step, shows a strong preference for the xanthophyll zeaxanthin in vitro and in bacterio. In order to investigate substrate specificity in planta and to establish a plant-based bio-factory system for crocin production, we compared wild-type Nicotiana benthamiana plants, accumulating various xanthophylls together with α- and β-carotene, with genome-edited lines, in which all the xanthophylls normally accumulated in leaves were replaced by a single xanthophyll, zeaxanthin. These plants were used as chassis for the production in leaves of saffron apocarotenoids (crocins, picrocrocin) using two transient expression methods to overexpress CsCCD2: agroinfiltration and inoculation with a viral vector derived from tobacco etch virus (TEV). The results indicated the superior performance of the zeaxanthin-accumulating line and of the use of the viral vector to express CsCCD2. The results also suggested a relaxed substrate specificity of CsCCD2 in planta, cleaving additional carotenoid substrates.

Published
2023

39. Deregulation of ζ‐carotene desaturase in Arabidopsis and tomato exposes a unique carotenoid‐derived redundant regulation of floral meristem identity and function

Author

McQuinn, Ryan P., primary, Leroux, Julie, additional, Sierra, Julio, additional, Escobar‐Tovar, Lina, additional, Frusciante, Sarah, additional, Finnegan, E. Jean, additional, Diretto, Gianfranco, additional, Giuliano, Giovanni, additional, Giovannoni, James J., additional, León, Patricia, additional, and Pogson, Barry J., additional

Published
2023
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41. Exploration of high‐throughput data for heat tolerance selection in Capsicum annuum

Author

Fumia, Nathan, primary, Kantar, Michael, additional, Lin, Ya‐ping, additional, Schafleitner, Roland, additional, Lefebvre, Véronique, additional, Paran, Ilan, additional, Börner, Andreas, additional, Diez, Maria José, additional, Prohens, Jaime, additional, Bovy, Arnaud, additional, Boyaci, Filiz, additional, Pasev, Gancho, additional, Tripodi, Pasquale, additional, Barchi, Lorenzo, additional, Giuliano, Giovanni, additional, and Barchenger, Derek W., additional

Published
2023
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43. A multi-omicNicotiana benthamianaresource for fundamental research and biotechnology

Author

Ranawaka, Buddhini, primary, An, Jiyuan, additional, Lorenc, Michał T., additional, Jung, Hyungtaek, additional, Sulli, Maria, additional, Aprea, Giuseppe, additional, Roden, Sally, additional, Hayashi, Satomi, additional, Cooper, Tal, additional, LeBlanc, Zacharie, additional, Llaca, Victor, additional, Orzaez, Diego, additional, Bombarely, Aureliano, additional, Bally, Julia, additional, Winefield, Christopher, additional, Giuliano, Giovanni, additional, and Waterhouse, Peter M., additional

Published
2022
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44. Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette

Author

Arrones, Andrea, primary, Mangino, Giulio, additional, Alonso, David, additional, Plazas, Mariola, additional, Prohens, Jaime, additional, Portis, Ezio, additional, Barchi, Lorenzo, additional, Giuliano, Giovanni, additional, Vilanova, Santiago, additional, and Gramazio, Pietro, additional

Published
2022
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45. Transcription factor SlBEL2 interferes with GOLDEN2‐LIKE and influences green shoulder formation in tomato fruits

Author

Niu, Xiao‐Lin, primary, Li, Hong‐Li, additional, Li, Rui, additional, Liu, Gang‐Shuai, additional, Peng, Zhen‐Zhen, additional, Jia, Wen, additional, Ji, Xiang, additional, Zhu, Hong‐Liang, additional, Zhu, Ben‐Zhong, additional, Grierson, Donald, additional, Giuliano, Giovanni, additional, Luo, Yun‐Bo, additional, and Fu, Da‐Qi, additional

Published
2022
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46. The genetic architecture of fruit quality and nutritional traits in Solanaceous crops

Author

Giuliano, Giovanni, Lefebvre, Véronique, Consortium, GtoPSOL, Agenzia Nazionale per le nuove Tecnologie, l’energia e lo sviluppo economico sostenibile = Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 677379,H2020,H2020-SFS-2015-2,G2P-SOL(2016), and European Project: 101000716,HARNESSTOM

Subjects
[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, pepper, eggplant, nutritional traits, Tomato
Abstract

International audience; In the frame of the G2P-SOL project, core collections representative of the worldwide genetic diversity of the four major Solanaceous crops (tomato, pepper, eggplant, potato) were created. These collections were phenotyped and subjected to metabolic profiling. Hundreds of novel metabolites have been identified and quantified, and QTLs have been mapped, both in the core collections and in segregating populations. The genetic architecture of some of these traits will be discussed in detail.

Published
2022

47. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Author

Denoeud, France, Carretero-Paulet, Lorenzo, Dereeper, Alexis, Droc, Gaëtan, Guyot, Romain, Pietrella, Marco, Zheng, Chunfang, Alberti, Adriana, Anthony, François, Aprea, Giuseppe, Aury, Jean-Marc, Bento, Pascal, Bernard, Maria, Bocs, Stéphanie, Campa, Claudine, Cenci, Alberto, Combes, Marie-Christine, Crouzillat, Dominique, Da Silva, Corinne, Daddiego, Loretta, De Bellis, Fabien, Dussert, Stéphane, Garsmeur, Olivier, Gayraud, Thomas, Guignon, Valentin, Jahn, Katharina, Jamilloux, Véronique, Joët, Thierry, Labadie, Karine, Lan, Tianying, Leclercq, Julie, Lepelley, Maud, Leroy, Thierry, Li, Lei-Ting, Librado, Pablo, Lopez, Loredana, Muñoz, Adriana, Noel, Benjamin, Pallavicini, Alberto, Perrotta, Gaetano, Poncet, Valérie, Pot, David, Rigoreau, Michel, Rouard, Mathieu, Rozas, Julio, Tranchant-Dubreuil, Christine, VanBuren, Robert, Zhang, Qiong, Andrade, Alan C., Argout, Xavier, Bertrand, Benoît, de Kochko, Alexandre, Graziosi, Giorgio, Henry, Robert J, Ming, Ray, Nagai, Chifumi, Rounsley, Steve, Sankoff, David, Giuliano, Giovanni, Albert, Victor A., Wincker, Patrick, and Lashermes, Philippe

Published
2014

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