272 results on '"Scalabrin, Simone"'
Search Results
2. A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
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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
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- 2024
- Full Text
- View/download PDF
3. Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought
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Eckert, Christian, Wildhagen, Henning, Paulo, Maria João, Scalabrin, Simone, Ballauff, Johannes, Schnabel, Sabine K, Vendramin, Vera, Keurentjes, Joost JB, Bogeat-Triboulot, Marie-Béatrice, Taylor, Gail, and Polle, Andrea
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Genetics ,Climate Change ,Droughts ,Gene Expression Regulation ,Plant ,Genotype ,Populus ,Transcriptome ,Water - Abstract
Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis.
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- 2022
4. Influence of the timing of periodontal intervention on periapical/periodontal repair in endodontic-periodontal lesions: a systematic review
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Friedrich, Fernanda, Scalabrin, Simone Argenta, Weissheimer, Theodoro, Rösing, Cassiano Kuchenbecker, Só, Gabriel Barcelos, da Rosa, Ricardo Abreu, and Só, Marcus Vinicius Reis
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- 2023
- Full Text
- View/download PDF
5. Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize
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Scaglione, Davide, Pinosio, Sara, Marroni, Fabio, Di Centa, Eleonora, Fornasiero, Alice, Magris, Gabriele, Scalabrin, Simone, Cattonaro, Federica, Taylor, Gail, and Morgante, Michele
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Biotechnology ,Human Genome ,Genetics ,Benchmarking ,Genotype ,Genotyping Techniques ,Humans ,Polymorphism ,Single Nucleotide ,Populus ,Reproducibility of Results ,Zea mays ,SPET ,Allegro ,genotyping-by-sequencing ,targeted genotyping ,bioenergy crops ,Populus nigra ,SNP ,GWAS ,Populus nigra ,Zea mays ,Ecology ,Plant Biology ,Forestry Sciences ,Plant Biology & Botany - Abstract
BACKGROUND AND AIMS:The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories. METHODS:Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits. KEY RESULTS:Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar. CONCLUSION:The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.
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- 2019
6. Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra
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Wildhagen, Henning, Paul, Shanty, Allwright, Mike, Smith, Hazel K, Malinowska, Marta, Schnabel, Sabine K, Paulo, M João, Cattonaro, Federica, Vendramin, Vera, Scalabrin, Simone, Janz, Dennis, Douthe, Cyril, Brendel, Oliver, Buré, Cyril, Cohen, David, Hummel, Irène, Le Thiec, Didier, van Eeuwijk, Fred, Keurentjes, Joost JB, Flexas, Jaume, Morgante, Michele, Robson, Paul, Bogeat-Triboulot, Marie-Béatrice, Taylor, Gail, and Polle, Andrea
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Genetics ,Droughts ,Gene Expression ,Genes ,Plant ,Genotype ,Hydrolysis ,Lignin ,Multigene Family ,Polysaccharides ,Populus ,Wood ,biofuels ,cell wall ,drought ,genotypic variation ,glucose release ,lignin ,saccharification ,wood traits ,Ecology ,Plant Biology ,Forestry Sciences ,Plant Biology & Botany - Abstract
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential. The three poplar genotypes differed in wood anatomy, lignin content and saccharification potential. Drought resulted in reduced cambial activity, decreased vessel and fiber lumina, and increased the saccharification potential. The saccharification potential was unrelated to lignin content as well as to most wood anatomical traits. RNA sequencing of the developing xylem revealed that 1.5% of the analyzed genes were differentially expressed in response to drought, while 67% differed among the genotypes. Weighted gene correlation network analysis identified modules of co-expressed genes correlated with saccharification potential. These modules were enriched in gene ontology terms related to cell wall polysaccharide biosynthesis and modification and vesicle transport, but not to lignin biosynthesis. Among the most strongly saccharification-correlated genes, those with regulatory functions, especially kinases, were prominent. We further identified transcription factors whose transcript abundances differed among genotypes, and which were co-regulated with genes for biosynthesis and modifications of hemicelluloses and pectin. Overall, our study suggests that the regulation of pectin and hemicellulose metabolism is a promising target for improving wood quality of second generation bioenergy crops. The causal relationship of the identified genes and pathways with saccharification potential needs to be validated in further experiments.
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- 2018
7. Mozambican Coffea accessions from Ibo and Quirimba Islands: identification and geographical distribution
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Navarini, Luciano, primary, Scaglione, Davide, additional, Del Terra, Lorenzo, additional, Scalabrin, Simone, additional, Mavuque, Lopes, additional, Turello, Luca, additional, Nguenha, Rafael, additional, and Luongo, Gianluca, additional
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- 2024
- Full Text
- View/download PDF
8. Diversity and enrichment of breeding material for resilience in European forests
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European Commission, Ministerio de Ciencia e Innovación (España), Olsson, Sanna [0000-0002-1199-4499], Dauphin, Benjamin [0000-0003-0982-4252], Jorge, Véronique [0000-0002-5016-3006], Grivet, Delphine [0000-0001-8168-4456], Farsakoglou, Anna Maria [0000-0002-1906-2813], Climent Maldonado, José María [0000-0002-0815-2645], Alizoti, Paraskevi [0000-0002-5656-8434], Faivre-Rampant, Patricia [0000-0003-0777-6621], Pinosio, S. [0000-0002-1820-3637], Scalabrin, Simone [0000-0001-8686-8385], Bagnoli, Francesca [0000-0001-6909-0006], Scotti, I. [0000-0002-8951-2680], Vendramin, G. G. [0000-0001-9921-7872], González-Martínez, S. C. [0000-0002-4534-3766], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Olsson, Sanna, Dauphin, Benjamin, Jorge, Véronique, Grivet, Delphine, Farsakoglou, Anna Maria, Climent Maldonado, José María, Alizoti, Paraskevi, Faivre-Rampant, Patricia, Pinosio, S., Milesi, Pascal, Scalabrin, Simone, Bagnoli, Francesca, Scotti, I., Vendramin, G. G., González-Martínez, Santiago C., Fady, Bruno, Aravanopoulos, Filippos A., Bastien, Catherine, Alía Miranda, Ricardo, European Commission, Ministerio de Ciencia e Innovación (España), Olsson, Sanna [0000-0002-1199-4499], Dauphin, Benjamin [0000-0003-0982-4252], Jorge, Véronique [0000-0002-5016-3006], Grivet, Delphine [0000-0001-8168-4456], Farsakoglou, Anna Maria [0000-0002-1906-2813], Climent Maldonado, José María [0000-0002-0815-2645], Alizoti, Paraskevi [0000-0002-5656-8434], Faivre-Rampant, Patricia [0000-0003-0777-6621], Pinosio, S. [0000-0002-1820-3637], Scalabrin, Simone [0000-0001-8686-8385], Bagnoli, Francesca [0000-0001-6909-0006], Scotti, I. [0000-0002-8951-2680], Vendramin, G. G. [0000-0001-9921-7872], González-Martínez, S. C. [0000-0002-4534-3766], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Olsson, Sanna, Dauphin, Benjamin, Jorge, Véronique, Grivet, Delphine, Farsakoglou, Anna Maria, Climent Maldonado, José María, Alizoti, Paraskevi, Faivre-Rampant, Patricia, Pinosio, S., Milesi, Pascal, Scalabrin, Simone, Bagnoli, Francesca, Scotti, I., Vendramin, G. G., González-Martínez, Santiago C., Fady, Bruno, Aravanopoulos, Filippos A., Bastien, Catherine, and Alía Miranda, Ricardo
- Abstract
Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if these new populations lack adaptability. Despite the long tradition of breeding activities in Europe, there is still a need to assess the impact of genetically enriched material on forests’ resilience. In this study, we address (1) the genetic diversity of selected material compared to its wild ancestors, and (2) how to enrich breeding material to support forests’ resilience under changing socio-environmental conditions. We analysed 16 study cases of selected material delivered from breeding activities in four European forest tree species (Pinus halepensis Mill., Pinus nigra J.F. Arnold, Pinus pinaster Ait. and Populus nigra L.) with different levels of breeding. To answer these two questions, we first assessed and compared the genetic diversity of selected material versus natural populations using both putatively neutral and adaptive (based on diverging selection) Single Nucleotide Polymorphisms (SNPs). We then suggest how to enrich these populations for resilience under future climatic conditions by defining a core collection for each species including material from populations that will likely disappear under future conditions. Thanks to the large SNP datasets available for our focal species, we were able to detect some trends in our data. Expected and observed heterozygosity values for selected populations were almost always identical. The selected material showed small but significant genetic differentiation from their original population and their inbreeding coefficient was generally lower. However, the level of genetic improvement (i.e. low vs high) was not correlated with the observed genetic differences between sele
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- 2023
9. A high‐density, SNP‐based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding
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Maccaferri, Marco, Ricci, Andrea, Salvi, Silvio, Milner, Sara Giulia, Noli, Enrico, Martelli, Pier Luigi, Casadio, Rita, Akhunov, Eduard, Scalabrin, Simone, Vendramin, Vera, Ammar, Karim, Blanco, Antonio, Desiderio, Francesca, Distelfeld, Assaf, Dubcovsky, Jorge, Fahima, Tzion, Faris, Justin, Korol, Abraham, Massi, Andrea, Mastrangelo, Anna Maria, Morgante, Michele, Pozniak, Curtis, N'Diaye, Amidou, Xu, Steven, and Tuberosa, Roberto
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Human Genome ,Genetics ,Biotechnology ,Breeding ,Chromosome Mapping ,Chromosomes ,Plant ,Genetic Linkage ,Genome ,Plant ,Genomics ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,Tetraploidy ,Triticum ,durum wheat ,single nucleotide polymorphism ,consensus map ,genomics-assisted breeding ,homeologous loci ,chromosome translocation events ,anchor markers ,Biological Sciences ,Technology ,Medical and Health Sciences - Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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- 2015
10. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
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Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F.
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Quantitative Biology - Genomics - Abstract
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets
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- 2013
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11. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
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Wu, G Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Del Fabbro, Cristian, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco R, Estornell, Leandro H, Muñoz-Sanz, Juan V, Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez-Pérez, Julián, Ramón, Daniel, Brunel, Dominique, Luro, François, Chen, Chunxian, Farmerie, William G, Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astúa, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel
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Base Sequence ,Breeding ,Citrus ,Conserved Sequence ,Crops ,Agricultural ,Evolution ,Molecular ,Genetic Variation ,Genome ,Plant ,Molecular Sequence Data ,Sequence Analysis ,DNA ,Species Specificity - Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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- 2014
12. Complex history of admixture during citrus domestication revealed by genome analysis
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Wu, G. Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Fabbro, Cristian Del, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco, Estornell, Leandro H., Mu?oz-Sanz, Juan V., Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez, Julián Pérez, Ramon, Daniel, Brunel, Dominique, Luro, Francois, Chen, Chunxian, Farmerie, William G., Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astua, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel
- Subjects
haploid Clementine mandarin ,C. maxima ,C. reticulata ,Mangshan ,China ,Huanglongbing ,apomixis via nucellar polyembryony ,ntrogressive hybridizations - Abstract
Although Citrus is the most globally significant tree fruit, its domestication history is poorlyunderstood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm.Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China showssubstantial sequence divergence from C. reticulata and appears to represent a distinct taxon.Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement.Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources ofvitamin C and other health-promoting compounds. Global production in 2012 exceeded 86million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly vulnerable to disease outbreaks, including citrus greening disease (also known as Huanglongbing) that is rapidly spreading throughout the world's major citrus producing regions1. Understanding the population genomics and domestication of citrus will enable strategies for improvements to citrus including resistance to greening and otherdiseases. The domestication and distribution of edible citrus types began several thousand years ago in Southeast Asia and spread globally following ancient land and sea routes. The lineages that gave rise to most modern cultivated varieties, however, are lost in undocumented antiquity, and their identities remain controversial2, 3. Several features of Citrus biology and cultivation make deciphering these origins difficult. Cultivated varieties are typically propagated clonally by grafting and through asexual seed production (apomixis via nucellar polyembryony) to maintain desirable combinations of traits (Fig. 1). Thus many important cultivar groups have characteristic basic genotypes that presumably arose through interspecific hybridization and/or successive introgressive hybridizations of wild ancestral species. These domestication events predated the global expansion of citrus cultivation by hundreds or perhaps thousands of years, with no record of the domestication process. Diversity within such groups arises through accumulated somatic mutations, generally without sexual recombination, either as limb sports on trees or variants among apomictic seedling progeny.Two wild species are believed to have contributed to domesticated pummelos, mandarins and oranges. Based on morphology and genetic markers, pummelos have generally been identified with the wild species C. maxima (Burm.) Merrill that is indigenous to Southeast Asia. Although mandarins are similarly widely identified with the species C. reticulata Blanco 4-6, wild populations of C. reticulata have not been definitively described. Various authors have taken dif
- Published
- 2014
13. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- Author
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Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F
- Abstract
Abstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
- Published
- 2013
14. Diversity and enrichment of breeding material for resilience in European forests
- Author
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Olsson, Sanna, Dauphin, Benjamin, Jorge, Veronique, Grivet, Delphine, Farsakoglou, Anna Maria, Climent, Jose, Alizoti, Paraskevi, Faivre-Rampant, Patricia, Pinosio, Sara, Milesi, Pascal, Scalabrin, Simone, Bagnoli, Francesca, Scotti, Ivan, Vendramin, Giovanni G., Gonzalez-Martinez, Santiago C., Fady, Bruno, Aravanopoulus, Filippos A., Bastien, Catherine, Alia, Ricardo, European Commission, Ministerio de Ciencia e Innovación (España), Olsson, Sanna, Dauphin, Benjamin, Jorge, Véronique, Grivet, Delphine, Farsakoglou, Anna Maria, Climent, José, Alizoti, Paraskevi, Faivre-Rampant, Patricia, Pinosio, Sara, Scalabrin, Simone, Bagnoli, Francesca, Scotti, Ivan, Vendramin, Giovanni G., Gonzalez-Martinez, Santiago C., Fady, Bruno, and Alia, Ricardo
- Subjects
Adaptability ,Skogsvetenskap ,Forest Science ,Genetics ,Climate change ,Forestry ,Genetik ,Management, Monitoring, Policy and Law ,Breeding ,Genetic resources ,Genetic diversity ,Nature and Landscape Conservation - Abstract
11 Pág., Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if these new populations lack adaptability. Despite the long tradition of breeding activities in Europe, there is still a need to assess the impact of genetically enriched material on forests’ resilience. In this study, we address (1) the genetic diversity of selected material compared to its wild ancestors, and (2) how to enrich breeding material to support forests’ resilience under changing socio-environmental conditions. We analysed 16 study cases of selected material delivered from breeding activities in four European forest tree species (Pinus halepensis Mill., Pinus nigra J.F. Arnold, Pinus pinaster Ait. and Populus nigra L.) with different levels of breeding. To answer these two questions, we first assessed and compared the genetic diversity of selected material versus natural populations using both putatively neutral and adaptive (based on diverging selection) Single Nucleotide Polymorphisms (SNPs). We then suggest how to enrich these populations for resilience under future climatic conditions by defining a core collection for each species including material from populations that will likely disappear under future conditions. Thanks to the large SNP datasets available for our focal species, we were able to detect some trends in our data. Expected and observed heterozygosity values for selected populations were almost always identical. The selected material showed small but significant genetic differentiation from their original population and their inbreeding coefficient was generally lower. However, the level of genetic improvement (i.e. low vs high) was not correlated with the observed genetic differences between selected material and natural populations.The genetic characterization of natural populations distributed across the species range, and the future projection of their range stability, made it possible to identify core-collections that would significantly enrich breeding populations under uncertain future environmental conditions., This work was supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 676876-Gentree “Optimizing the management and sustainable use of forest genetic resources in Europe”; the Spanish Ministry of Science [Grant No RTI2018-094691-B-C32].
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- 2023
15. Effect of ultrasonic activation on the physicochemical properties and chemical composition of calcium silicate sealers
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Só, Gabriel Barcelos, primary, Scalabrin, Simone Argenta, additional, Hashizume, Lina Naomi, additional, Weissheimer, Theodoro, additional, Pereira, Jefferson, additional, Kuga, Milton, additional, rosa, ricardo, additional, and Só, Marcus Vinícius, additional
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- 2023
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16. Genome Sequencing, Transcriptomics, and Proteomics
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Muleo, Rosario, Morgante, Michele, Cattonaro, Federica, Scalabrin, Simone, Cavallini, Andrea, Natali, Lucia, Perrotta, Gaetano, Lopez, Loredana, Velasco, Riccardo, Kalaitzis, Panagiotis, Kole, Chittaranjan, Series editor, Rugini, Eddo, editor, Baldoni, Luciana, editor, Muleo, Rosario, editor, and Sebastiani, Luca, editor
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- 2016
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17. The functional capacity of plantaricin-producing Lactobacillus plantarum SF9C and S-layer-carrying Lactobacillus brevis SF9B to withstand gastrointestinal transit
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Butorac, Katarina, Banić, Martina, Novak, Jasna, Leboš Pavunc, Andreja, Uroić, Ksenija, Durgo, Ksenija, Oršolić, Nada, Kukolj, Marina, Radović, Slobodanka, Scalabrin, Simone, Žučko, Jurica, Starčević, Antonio, Šušković, Jagoda, and Kos, Blaženka
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- 2020
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18. 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
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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
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- 2020
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19. Hierarchical Assembly of Pools
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Vicedomini, Riccardo, Vezzi, Francesco, Scalabrin, Simone, Arvestad, Lars, Policriti, Alberto, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor
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- 2015
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20. CNV and Structural Variation in Plants: Prospects of NGS Approaches
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Francia, Enrico, Pecchioni, Nicola, Policriti, Alberto, Scalabrin, Simone, Sablok, Gaurav, editor, Kumar, Sunil, editor, Ueno, Saneyoshi, editor, Kuo, Jimmy, editor, and Varotto, Claudio, editor
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- 2015
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21. Diversity and enrichment of breeding material for resilience in European forests
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Olsson, Sanna, primary, Dauphin, Benjamin, additional, Jorge, Véronique, additional, Grivet, Delphine, additional, Farsakoglou, Anna Maria, additional, Climent, Jose, additional, Alizoti, Paraskevi, additional, Faivre-Rampant, Patricia, additional, Pinosio, Sara, additional, Milesi, Pascal, additional, Scalabrin, Simone, additional, Bagnoli, Francesca, additional, Scotti, Ivan, additional, Vendramin, Giovanni G., additional, Gonzalez-Martinez, Santiago C., additional, Fady, Bruno, additional, Aravanopoulus, Filippos A., additional, Bastien, Catherine, additional, and Alia, Ricardo, additional
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- 2023
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22. Between but not within species variation in the distribution of fitness effects
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James, Jennifer, Kastally, Chedly, Budde, Katharina B., González-Martínez, Santiago C., Milesi, Pascal, Pyhäjärvi, Tanja, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, Lascoux, Martin, James, Jennifer, Kastally, Chedly, Budde, Katharina B., González-Martínez, Santiago C., Milesi, Pascal, Pyhäjärvi, Tanja, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, and Lascoux, Martin
- Abstract
New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
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- 2023
23. The limits and potential of paleogenomic techniques for reconstructing grapevine domestication
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Wales, Nathan, Ramos Madrigal, Jazmín, Cappellini, Enrico, Carmona Baez, Aldo, Samaniego Castruita, José Alfredo, Romero-Navarro, J. Alberto, Carøe, Christian, Ávila-Arcos, María C., Peñaloza, Fernando, Moreno-Mayar, J. Víctor, Gasparyan, Boris, Zardaryan, Diana, Bagoyan, Tamara, Smith, Alexia, Pinhasi, Ron, Bosi, Giovanna, Fiorentino, Girolamo, Grasso, Anna Maria, Celant, Alessandra, Bar-Oz, Guy, Tepper, Yotam, Hall, Allan, Scalabrin, Simone, Miculan, Mara, Morgante, Michele, Di Gaspero, Gabriele, and Gilbert, M. Thomas P.
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- 2016
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24. The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing
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Royer, Mathilde, Cohen, David, Aubry, Nathalie, Vendramin, Vera, Scalabrin, Simone, Cattonaro, Federica, Bogeat-Triboulot, Marie-Béatrice, and Hummel, Irène
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- 2016
25. Genetic Diversity in the Grapevine Germplasm
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Cattonaro, Federica, Testolin, Raffaele, Scalabrin, Simone, Morgante, Michele, Gaspero, Gabriele Di, Tuberosa, Roberto, editor, Graner, Andreas, editor, and Frison, Emile, editor
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- 2014
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26. Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
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Vendramin, Vera, Ormanbekova, Danara, Scalabrin, Simone, Scaglione, Davide, Maccaferri, Marco, Martelli, Pierluigi, Salvi, Silvio, Jurman, Irena, Casadio, Rita, Cattonaro, Federica, Tuberosa, Roberto, Massi, Andrea, and Morgante, Michele
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- 2019
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27. Influence of the timing of periodontal intervention on periapical/periodontal repair in endodontic-periodontal lesions: a systematic review
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Friedrich, Fernanda, primary, Scalabrin, Simone Argenta, additional, Weissheimer, Theodoro, additional, Rösing, Cassiano Kuchenbecker, additional, Só, Gabriel Barcelos, additional, da Rosa, Ricardo Abreu, additional, and Só, Marcus Vinicius Reis, additional
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- 2022
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28. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species
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Dettori, Maria Teresa, Micali, Sabrina, Giovinazzi, Jessica, Scalabrin, Simone, Verde, Ignazio, and Cipriani, Guido
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- 2015
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29. A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat
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Rustenholz, Camille, Choulet, Frédéric, Laugier, Christel, Šafář, Jan, Šimková, Hana, Doležel, Jaroslav, Magni, Federica, Scalabrin, Simone, Cattonaro, Federica, Vautrin, Sonia, Bellec, Arnaud, Bergès, Hélène, Feuillet, Catherine, and Paux, Etienne
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- 2011
30. Hierarchical Assembly of Pools
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Vicedomini, Riccardo, primary, Vezzi, Francesco, additional, Scalabrin, Simone, additional, Arvestad, Lars, additional, and Policriti, Alberto, additional
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- 2015
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31. Durum Wheat Pan-Transcriptome as a Bridge to Unravel Tetraploid and Hexaploid Wheat Gene Function and Evolution
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ORMANBEKOVA Danara, MACCAFERRI Marco, TWARDZIOK Swen O, SCAGLIONE Davide, VENDRAMIN Vera, SCALABRIN Simone, CORNETI Simona, BOZZOLI Matteo, MASSI Andrea, MAYER Klaus FX, MORGANTE Michele, POZNIAK Curtis, TUBEROSA Roberto, and ORMANBEKOVA Danara, MACCAFERRI Marco, TWARDZIOK Swen O, SCAGLIONE Davide, VENDRAMIN Vera, SCALABRIN Simone, CORNETI Simona, BOZZOLI Matteo, MASSI Andrea, MAYER Klaus FX, MORGANTE Michele, POZNIAK Curtis, TUBEROSA Roberto
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wheat, single nucleotide polymorphisms, pan-transcriptome, genomics - Abstract
This study presents the transcriptome analysis of 13 elite durum wheat varieties representatives of the worldwide cultivated germplasm. cDNA libraries were produced from roots, seedling leaves and developing grains. Based on the reference genome sequence assembly of durum wheat cv. Svevo, 75.0, 70.5 and 74.5% of high-confidence Svevo genes were expressed in grain, leaf and root, respectively. Principal Component Analysis (PCA) showed a gene expression clustering led by tissues and varietal ancestry. Differentially up- and down-regulated gene clusters based on tissues and varieties were identified. Functional enrichment analysis for three Gene Ontology terms showed that differentially expressed genes were significantly enriched in transport, kinase activity, binding, enzyme activity and protein metabolism. Variance expression analysis projected on the Svevo assembly revealed the chromosome regions that drove the major expression variation patterns. Clustering the gene expression profiles and the cultivar’s expression profiles evidenced several gene expression patterns related to their co-ancestry, particularly for the grain. Towards a more complete assembly of a pan-transcriptome in durum, the cultivar-specific reads that could not be mapped on the Svevo genome (4-30% referred to Svevo Illumina sequencing data) are being de novo assembled. Further, using the transcriptome of the 13 varieties in relation to bread wheat reference genome (cv. Chinese Spring IWGSC RefSeq) we are currently investigating the gene loss/deletion during the polyploidisation events. Moreover, the availability of the genome assemblies of the 10+ Wheat Genomes Project, which includes cultivars that represent genetic diversity, will allow us to infer strong allele fixation events (allopolyploidisation bottleneck).
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- 2020
32. Genetic Diversity in the Grapevine Germplasm
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Cattonaro, Federica, primary, Testolin, Raffaele, additional, Scalabrin, Simone, additional, Morgante, Michele, additional, and Gaspero, Gabriele Di, additional
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- 2013
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33. 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
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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
34. Additional file 2 of The functional capacity of plantaricin-producing Lactobacillus plantarum SF9C and S-layer-carrying Lactobacillus brevis SF9B to withstand gastrointestinal transit
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Butorac, Katarina, Banić, Martina, Novak, Jasna, Pavunc, Andreja Leboš, Uroić, Ksenija, Durgo, Ksenija, Oršolić, Nada, Kukolj, Marina, Radović, Slobodanka, Scalabrin, Simone, Žučko, Jurica, Starčević, Antonio, Šušković, Jagoda, and Kos, Blaženka
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food and beverages - Abstract
Additional file 2: Table S1. Genes of Lb. plantarum SF9C involved in plantaricin production and their known or putative biochemical functions.
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- 2020
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35. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla: the French-Italian public consortium for grapevine genome characterization
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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 [...]
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- 2007
36. Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach
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Falchi, Rachele, Vendramin, Elisa, Zanon, Laura, Scalabrin, Simone, Cipriani, Guido, Verde, Ignazio, Vizzotto, Giannina, and Morgante, Michele
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- 2013
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37. A physical, genetic and functional sequence assembly of the barley genome
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Mayer, Klaus F. X., Waugh, Robbie, Langridge, Peter, Close, Timothy J., Wise, Roger P., Graner, Andreas, Matsumoto, Takashi, Sato, Kazuhiro, Schulman, Alan, Muehlbauer, Gary J., Stein, Nils, Ariyadasa, Ruvini, Schulte, Daniela, Poursarebani, Naser, Zhou, Ruonan, Steuernagel, Burkhard, Mascher, Martin, Scholz, Uwe, Shi, Bujun, Madishetty, Kavitha, Svensson, Jan T., Bhat, Prasanna, Moscou, Matthew, Resnik, Josh, Hedley, Pete, Liu, Hui, Morris, Jenny, Frenkel, Zeev, Korol, Avraham, Bergès, Hélène, Stein, Nils, Taudien, Stefan, Felder, Marius, Groth, Marco, Platzer, Matthias, Himmelbach, Axel, Lonardi, Stefano, Duma, Denisa, Alpert, Matthew, Cordero, Francesa, Beccuti, Marco, Ciardo, Gianfranco, Ma, Yaqin, Wanamaker, Steve, Close, Timothy J., Cattonaro, Federica, Vendramin, Vera, Scalabrin, Simone, Radovic, Slobodanka, Wing, Rod, Morgante, Michele, Waugh, Robbie, Nussbaumer, Thomas, Gundlach, Heidrun, Martis, Mihaela, Poland, Jesse, Mayer, Klaus F. X., Spannagl, Manuel, Pfeifer, Matthias, Moisy, Cédric, Tanskanen, Jaakko, Zuccolo, Andrea, Mayer, Klaus F. X., Schulman, Alan, Russell, Joanne, Druka, Arnis, Marshall, David, Bayer, Micha, Swarbreck, David, Sampath, Dharanya, Ayling, Sarah, Febrer, Melanie, Caccamo, Mario, Tanaka, Tsuyoshi, Wannamaker, Steve, Schmutzer, Thomas, Waugh, Robbie, Brown, John W. S., and Fincher, Geoffrey B.
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- 2012
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38. Colonisation potential of plantaricin-producing Lactobacillus plantarum SF9C andS-layer-carrying Lactobacillus brevis SF9B among gut microbiota
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Butorac, Katarina, primary, Banic, Martina, additional, Novak, Jasna, additional, Pavunc, Andreja Leboš, additional, Uroic, Ksenija, additional, Orsolic, Nada, additional, Kukolj, Marina, additional, Radovic, Slobodanka, additional, Scalabrin, Simone, additional, Zucko, Jurica, additional, Starčevic, Antonio, additional, Suskovic, Jagoda, additional, and Kos, Blaženka, additional
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- 2020
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39. Colonization potential of plantaricin-producing Lactobacillus plantarum SF9C and S-layer carrying Lactobacillus brevis SF9B among gut microbiota
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Butorac, Katarina, primary, Banic, Martina, additional, Novak, Jasna, additional, Pavunc, Andreja Leboš, additional, Uroic, Ksenija, additional, Orsolic, Nada, additional, Kukolj, Marina, additional, Radovic, Slobodanka, additional, Scalabrin, Simone, additional, Zucko, Jurica, additional, Starčevic, Antonio, additional, Suskovic, Jagoda, additional, and Kos, Blaženka, additional
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- 2020
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40. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker
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Mariotti, Roberto, primary, Fornasiero, Alice, additional, Mousavi, Soraya, additional, Cultrera, Nicolò G.M., additional, Brizioli, Federico, additional, Pandolfi, Saverio, additional, Passeri, Valentina, additional, Rossi, Martina, additional, Magris, Gabriele, additional, Scalabrin, Simone, additional, Scaglione, Davide, additional, Di Gaspero, Gabriele, additional, Saumitou-Laprade, Pierre, additional, Vernet, Philippe, additional, Alagna, Fiammetta, additional, Morgante, Michele, additional, and Baldoni, Luciana, additional
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- 2020
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41. Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of ‘Lito’ Chromosome 1 and Analysis of Candidate Genes
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De Mori, Gloria, primary, Falchi, Rachele, additional, Testolin, Raffaele, additional, Bassi, Daniele, additional, Savazzini, Federica, additional, Dondini, Luca, additional, Tartarini, Stefano, additional, Palmisano, Francesco, additional, Minafra, Angelantonio, additional, Spadotto, Alessandro, additional, Scalabrin, Simone, additional, and Geuna, Filippo, additional
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- 2019
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42. Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine
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Foria, Serena, primary, Copetti, Dario, additional, Eisenmann, Birgit, additional, Magris, Gabriele, additional, Vidotto, Michele, additional, Scalabrin, Simone, additional, Testolin, Raffaele, additional, Cipriani, Guido, additional, Wiedemann‐Merdinoglu, Sabine, additional, Bogs, Jochen, additional, Di Gaspero, Gabriele, additional, and Morgante, Michele, additional
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- 2019
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43. Additional file 15: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
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Vendramin, Vera, Ormanbekova, Danara, Scalabrin, Simone, Scaglione, Davide, Maccaferri, Marco, Martelli, Pierluigi, Salvi, Silvio, Jurman, Irena, Casadio, Rita, Cattonaro, Federica, Tuberosa, Roberto, Massi, Andrea, and Morgante, Michele
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Figure S5. Functional analysis of transcripts with >â 90% coverage andâ >â 50% identity. Number of sequences with the corresponding A) Molecular Function B) Biological Process C) Cellular Component. (PDF 24 kb)
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- 2019
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44. Additional file 6: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
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Vendramin, Vera, Ormanbekova, Danara, Scalabrin, Simone, Scaglione, Davide, Maccaferri, Marco, Martelli, Pierluigi, Salvi, Silvio, Jurman, Irena, Casadio, Rita, Cattonaro, Federica, Tuberosa, Roberto, Massi, Andrea, and Morgante, Michele
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Figure S3. Validation of assemblies. The best assembly was validated versus two datasets: (A) full-length cDNAs [11, 23]; (B) Triticum aestivum chromosome 3B genes. Bars represent the percentage of genes reconstructed at least in 80% of their length. Different colors represent the number of different contigs necessary to reconstruct the genes. (PDF 104 kb)
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- 2019
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45. Additional file 5: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
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Vendramin, Vera, Ormanbekova, Danara, Scalabrin, Simone, Scaglione, Davide, Maccaferri, Marco, Martelli, Pierluigi, Salvi, Silvio, Jurman, Irena, Casadio, Rita, Cattonaro, Federica, Tuberosa, Roberto, Massi, Andrea, and Morgante, Michele
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Figure S2. Evaluation of de novo assemblies. Comparison at different k-mer values (i.e. k41, k51, k61, k64) and with different tools among different assemblies. (A) and (B) refer to assemblies computed with CLC and indicate, respectively, number of contigs and N50. (C) and (D) refer to Velvet-Oases assemblies. (PDF 601 kb)
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- 2019
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46. Tradicionalno proizvedeni fermentirani mliječni proizvodi kao bogat izvor korisnih bakterija s pozitivnim utjecajem na zdravlje čovjeka
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Kos, Blaženka, Šušković, Jagoda, Novak, Jasna, Leboš Pavunc, Andreja, Uroić, Ksenija, Zorić, Katarina, Banić, Martina, Oršolić, Nada, Kazazić, Saša, Kazazić, Snježana, Radović, Slobodanka, Scalabrin, Simone, Cescutti, Paola, Bellich, Barbara, and Volarić, Vera
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autohtone bakterije mliječne kiseline ,tradicionalni fermentirani mliječni proizvodi, intestinalna mikrobiota ,farmabiotici ,živi bioterapijski lijekovi - Abstract
Zbirka autohtonih bakterija mliječne kiseline (BMK) Laboratorija za tehnologiju antibiotika, enzima, probiotika i starter kultura, Prehrambeno-biotehnološkog fakulteta Sveučilišta u Zagrebu, sadrži više od 200 sojeva BMK. Većina je bakterijskih sojeva izolirana iz tradicionalno proizvedenih fermentiranih mliječnih proizvoda, identificirana 16S rDNA sekvencioniranjem i selekcionirana na temelju strogih izbornih probiotičkih kriterija. Istraživanja koja se provode na nacionalnom znanstvenom projektu “Probiotici i starter kulture – površinski proteini i bakteriocini”, kojeg financira Hrvatska zaklada za znanost (HRZZ), imaju za cilj odabir i karakterizaciju „nove generacije probiotika“, bakterijskih sojeva sa specifičnim svojstvima, kao što su proizvodnja površinskih S-proteina, peptida s antibakterijskom aktivnošću - bakteriocina, egzopolisaharida i proteolitičkih enzima. Odabrani autohtoni sojevi BMK su okarakterizirani fiziološkim testovima, analizom sekvencioniranih genoma, te LC-MS/MS i NMR analizama, u svrhu definiranja njihovog specifičnog metabolizamskog potencijala. Prema dobivenim rezultatima, tradicionalno proizvedeni fermentirani mliječni proizvodi su bogat izvor korisnih bakterija mliječne kiseline koje mogu svojom specifičnom metabolizamskom aktivnošću pozitivno utjecati na raznolikost i sastav crijevne mikrobiote što je prepoznato kao preduvjet održavanja intestinalnog trakta zdravim. Velik potencijal probiotika kao “živih lijekova” prepoznat je u terapiji disbioze i ponovnom uspostavljanju narušene ravnoteže crijevne mikrobiote, koja je “zlatni cilj” terapije i “ključni senzor” okolišnih čimbenika koji uzrokuju metabolizamske poremećaje i kronične bolesti kod ljudi. Osim toga, promjene u sastavu intestinalne mikrobiote mogu utjecati na raspoloženje, a mogu uzrokovati i promjenu u fenotipu, od pretilosti do standardne tjelesne mase. Stoga prehrambene i farmaceutske tvrtke osnivaju istraživačke centre mikrobioma za ravoj probiotika kao lijekova koje US FDA naziva „živi bioterapijski pripravci“ (engl. „live biotherapeutic products (LBPs)“), a europska industrija „farmabiotici“ (engl. „pharmabiotics“). Analitičari predviđaju vrijednost tržišta „živih bioterapijskih pripravaka“ veću od 500 milijuna EUR do 2030. godine.
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- 2018
47. Odabir autohtonih starter kultura sa specifičnim metabolizamskim svojstvima za proizvodnju sušenog sira
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Zorić, Katarina, Banić, Martina, Vidulin, Tina, Tonković, Katarina, Leboš Pavunc, Andreja, Novak, Jasna, Uroić, Ksenija, Kazazić, Saša, Kazazić, Snježana, Radović, Slobodanka, Scalabrin, Simone, Cesutti, Paola, Bellich, Barbara, Gregurek, Ljerka, Šušković, Jagoda, and Kos, Blaženka.
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S-proteini, bakteriocini, egzopolisaharidi, proteolitička aktivnost, probiotici - Abstract
Tradicionalno proizvedeni sirevi su bogat izvor autohtonih sojeva bakterija mliječne kiseline (BMK) sa specifičnim metabolizamskim svojstvima, kao što su proizvodnja S-proteina, bakteriocina, egzopolisaharida i proteolitičkih enzima. Stoga su izolirani sojevi BMK odabrani prema strogo definiranom probiotičkim kriterijima, a njihova identifikacija je provedena 16S rDNA sekvencioniranjem i sekvencioniranjem cijelog genoma. S-proteini okarakterizirani su SDS-PAGE i LC-MS/MS analizama. Geni za proizvodnju bakteriocina su identificirani primjenom PCR-a (eng. Polymerase Chain Reaction) sa specifičnim početnicama, dok je bakteriocinska aktivnost ispitana metodom dvostrukog sloja i združenim uzgojem sa Staphylococcus aureus 3048 i Listeria monocytogenes ATCC19111. Soj Lactobacillus fermentum D12 proizvodi egzopolisaharide, a selekcioniran je na temelju specifičnog fenotipa „formiranja dugih rastezljivih niti“ (tzv. „ropy“ fenotip) poraslih kolonija na čvrstoj hranjivoj podlozi obogaćenoj ugljikohidratima. Sastav i struktura tri proizvedena egzopolisaharida određeni su GC, GC/MS, 1H-NMR i 2D-NMR analizama. Proteolitička aktivnost ispitana je Ansonovom, Tricine-SDS-PAGE i LC-MS/MS metodama, dok su geni za proteolitičke enzime detektirani primjenom PCR-a sa specifičnim početnicama. Na temelju provedenih istraživanja, odabrana su četiri soja BMK kao autohtone starter kulture za proizvodnju dimljenog sira ; Lactococcus lactis ZG7-10, Lactobacillus brevis D6, Lactobacillus plantarum D13 i Lactobacillus fermentum D12.
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- 2018
48. Combined probiotic effect of S-layer-carrying Lactobacillus brevis SF9B and bacteriocin- expressing Lactobacillus plantarum SF9C strains on faecal microbiota of rats
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Zorić, Katarina, Banić, Martina, Uroić, Ksenija, Leboš Pavunc, Andreja, Novak, Jasna, Durgo, Ksenija, Oršolić, Nada, Kukolj, Marina, Petković, Hrvoje, Jamnik, Polona, Kazazić, Saša, Kazazić, Snježana, Radović, Slobodanka, Scalabrin, Simone, Šušković, Jagoda, Kos, Blaženka., and Kovačević Ganić, Karin
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food and beverages ,co-culture ,S-layer ,probiotic ,bacteriocin ,microbiota - Abstract
The aim of this study was to assess the probiotic potential of two Lactobacillus strains naturally occurring as a co-culture in the spontaneous fermented Croatian white cabbage cultivar Varaždinski. The automatic RAST annotation of their whole genome sequences obtained by Illumina MiSeq platform, and tblastn v.2.2.27 comparison of the assembled contigs with the sequences deposited in NCBI, revealed the presence of bacteriocin- encoding genes in the genome of L. plantarum SF9C and surface layer protein (Slp) genes in the genome of Lactobacillus brevis SF9B. Slp may act as an adhesin and contribute to the antimicrobial activity against the pathogens with whom the carrying strain competes for the same adhesion sites. The ability of SF9B cells to compete and exclude Gram-negative pathogens Escherichia coli 3014 and Salmonella enterica serovar Typhimurium FP1 using Caco-2 cell line was hereby confirmed. Moreover, the antimicrobial activity of L. plantarum SF9C against Gram- positive pathogens L. monocytogenes ATCC 19111 and S. aureus 3048 was verified using agar- spot, well diffusion and co- cultivation assay. Moreover, the combined probiotic effect of oral administration of the two Lactobacillus strains on fecal microbiota composition of rats was established.
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- 2018
49. The role of S-layer proteins as one of the most abundant biopolymers on Earth in probiotic properties of bacterial strain Lactobacillus brevis SF9B
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Zorić, Katarina, Kos, Blaženka, Banić, Martina, Uroić, Ksenija, Leboš Pavunc, Andreja, Novak, Jasna, Durgo, Ksenija, Petković, Hrvoje, Jamnik, Polona, Kazazić, Saša, Kazazić, Snježana, Radović, Slobodanka, Scalabrin, Simone, Hynӧnen, Ulla, and Šušković, Jagoda.
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S-layer proteins ,Lactobacillus brevis ,probiotic culture - Abstract
Surface (S)-layer proteins (Slps) form crystalline arrays of protein subunits as the outermost component of the cell wall in only few strains of Lactobacillus genera. In the genome of Lactobacillus brevis SF9B strain, three regions showed high homology with following slp sequences of the reference strain L. brevis ATCC 14869: with SlpB and SlpC in contig 2 (percentage of identities 65% and 89%, respectively) and with SlpD in contig 32 (percentage of identities 99%). Using SDS-PAGE of GHCl-extracted surface proteins of SF9B, a 50 kDa protein band, indicating the expression of the presumed Slp, was detected. 2D- PAGE of the same protein sample revealed a spot with isoelectric point and molecular weight of approximately 10, and 50 kDa, respectively. Structure and function prediction of the isolated Slp was generated using I-TASSER server, based on the data available for L. brevis ATCC 14869. Since Slps are exposed at the cell surface of certain Lactobacillus strains, they represent an interface between the bacterium and its biotic and abiotic microenvironments. Considering the fact that these environments include stress conditions which can affect bacterial viability and activity in the intestinal tract, Slps must have great importance in probiotic properties of the bacterial cells which express them. Although Slps of Lactobacillus strains are of great research interest for number of years, their physiological function remained poorly understood. However, Slps of strain SF9B mediate bacterial adherence to mucin, Caco-2 cells and extracellular matrix proteins, increase survival of L. brevis SF9B cells in simulated gastrointestinal conditions and during freeze- drying, and enhance their aggregation and coaggregation ability, which are important probiotic properties. The above mentioned results indicate that Slps contribute to technological and probiotic properties of strain L. brevis SF9B and that they have great role in potential application of that strain as novel probiotic culture.
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- 2018
50. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar
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Jurman Irena, Faes Giorgia, Marconi Raffaella, Malacarne Giulia, Prete Giacomo, Coppola Giuseppina, Felice Nicoletta, Pindo Massimo, Moroldo Marco, Troggio Michela, Scalabrin Simone, Grando Stella, Jesse Taco, Segala Cinzia, Valle Giorgio, Policriti Alberto, Fontana Paolo, Morgante Michele, and Velasco Riccardo
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. Results We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. Conclusions We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.
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- 2010
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