15 results on '"Cestaro Alessandro"'
Search Results
2. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies
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Jung Sook, Cestaro Alessandro, Troggio Michela, Main Dorrie, Zheng Ping, Cho Ilhyung, Folta Kevin M, Sosinski Bryon, Abbott Albert, Celton Jean-Marc, Arús Pere, Shulaev Vladimir, Verde Ignazio, Morgante Michele, Rokhsar Daniel, Velasco Riccardo, and Sargent Daniel
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Rosaceae ,Comparative genomics ,Evolution ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Results Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Conclusion Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.
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- 2012
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3. Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor
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Pilati Stefania, Cestaro Alessandro, Gatto Pamela, Zamboni Anita, Viola Roberto, Mattivi Fulvio, Moser Claudio, and Velasco Riccardo
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background In response to pathogen attack, grapevine synthesizes phytoalexins belonging to the family of stilbenes. Grapevine cell cultures represent a good model system for studying the basic mechanisms of plant response to biotic and abiotic elicitors. Among these, modified β-cyclodextrins seem to act as true elicitors inducing strong production of the stilbene resveratrol. Results The transcriptome changes of Vitis riparia × Vitis berlandieri grapevine cells in response to the modified β-cyclodextrin, DIMEB, were analyzed 2 and 6 h after treatment using a suppression subtractive hybridization experiment and a microarray analysis respectively. At both time points, we identified a specific set of induced genes belonging to the general phenylpropanoid metabolism, including stilbenes and hydroxycinnamates, and to defence proteins such as PR proteins and chitinases. At 6 h we also observed a down-regulation of the genes involved in cell division and cell-wall loosening. Conclusions We report the first large-scale study of the molecular effects of DIMEB, a resveratrol inducer, on grapevine cell cultures. This molecule seems to mimic a defence elicitor which enhances the physical barriers of the cell, stops cell division and induces phytoalexin synthesis.
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- 2009
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4. Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
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Dal Ri Antonio, Fontana Paolo, Demattè Lorenzo, Cestaro Alessandro, Malossini Andrea, Perazzolli Michele, Pilati Stefania, Viola Roberto, Velasco Riccardo, and Moser Claudio
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact. Despite this relevance, little is known about the transcriptional changes and the regulatory circuits underlying the biochemical and physical changes occurring during berry development. Results Fruit ripening in the non-climacteric crop species Vitis vinifera L. has been investigated at the transcriptional level by the use of the Affymetrix Vitis GeneChip® which contains approximately 14,500 unigenes. Gene expression data obtained from berries sampled before and after véraison in three growing years, were analyzed to identify genes specifically involved in fruit ripening and to investigate seasonal influences on the process. From these analyses a core set of 1477 genes was found which was similarly modulated in all seasons. We were able to separate ripening specific isoforms within gene families and to identify ripening related genes which appeared strongly regulated also by the seasonal weather conditions. Transcripts annotation by Gene Ontology vocabulary revealed five overrepresented functional categories of which cell wall organization and biogenesis, carbohydrate and secondary metabolisms and stress response were specifically induced during the ripening phase, while photosynthesis was strongly repressed. About 19% of the core gene set was characterized by genes involved in regulatory processes, such as transcription factors and transcripts related to hormonal metabolism and signal transduction. Auxin, ethylene and light emerged as the main stimuli influencing berry development. In addition, an oxidative burst, previously not detected in grapevine, characterized by rapid accumulation of H2O2 starting from véraison and by the modulation of many ROS scavenging enzymes, was observed. Conclusion The time-course gene expression analysis of grapevine berry development has identified the occurrence of two well distinct phases along the process. The pre-véraison phase represents a reprogramming stage of the cellular metabolism, characterized by the expression of numerous genes involved in hormonal signalling and transcriptional regulation. The post-véraison phase is characterized by the onset of a ripening-specialized metabolism responsible for the phenotypic traits of the ripe berry. Between the two phases, at véraison, an oxidative burst and the concurrent modulation of the anti-oxidative enzymatic network was observed. The large number of regulatory genes we have identified represents a powerful new resource for dissecting the mechanisms of fruit ripening control in non-climacteric plants.
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- 2007
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5. Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
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Malacrida Giorgio, Cestaro Alessandro, Simonato Francesca, D'Angelo Michela, Lauro Federico M, Vitulo Nicola, Vezzi Alessandro, Campanaro Stefano, Bertoloni Giulio, Valle Giorgio, and Bartlett Douglas H
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. Results These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. Conclusion These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.
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- 2005
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6. Exploration of alternative splicing events in ten different grapevine cultivars.
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Potenza, Emilio, Racchi, Milvia Luisa, Sterck, Lieven, Coller, Emanuela, Asquini, Elisa, Tosatto, Silvio C. E., Velasco, Riccardo, Van de Peer, Yves, and Cestaro, Alessandro
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GENETIC regulation ,GENETIC engineering ,PLANT genes ,NUCLEOTIDE sequencing ,GENETICS - Abstract
Background: The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results: Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions: Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. [ABSTRACT FROM AUTHOR]
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- 2015
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7. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh).
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Bianco, Luca, Cestaro, Alessandro, Sargent, Daniel James, Banchi, Elisa, Derdak, Sophia, Di Guardo, Mario, Salvi, Silvio, Jansen, Johannes, Viola, Roberto, Gut, Ivo, Laurens, Francois, Chagné, David, Velasco, Riccardo, van de Weg, Eric, and Troggio, Michela
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GENOMES , *PLANT breeding , *APPLES , *PLANT germplasm , *SINGLE nucleotide polymorphisms ,APPLE genetics - Abstract
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ∼15.8 K SNP markers were mapped with an average of ∼6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs. [ABSTRACT FROM AUTHOR]
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- 2014
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8. The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’).
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Chagné, David, Crowhurst, Ross N., Pindo, Massimo, Thrimawithana, Amali, Deng, Cecilia, Ireland, Hilary, Fiers, Mark, Dzierzon, Helge, Cestaro, Alessandro, Fontana, Paolo, Bianco, Luca, Lu, Ashley, Storey, Roy, Knäbel, Mareike, Saeed, Munazza, Montanari, Sara, Kim, Yoon Kyeong, Nicolini, Daniela, Larger, Simone, and Stefani, Erika
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COMMON pear ,NUCLEOTIDE sequence ,PLANT genomes ,SINGLE nucleotide polymorphisms ,PLANT cell walls - Abstract
We present a draft assembly of the genome of European pear (Pyrus communis) ‘Bartlett’. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of ‘Louise Bonne de Jersey’ and ‘Old Home’. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus×domestica). The ‘Bartlett’ genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development. [ABSTRACT FROM AUTHOR]
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- 2014
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9. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin.
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Troggio, Michela, Šurbanovski, Nada, Bianco, Luca, Moretto, Marco, Giongo, Lara, Banchi, Elisa, Viola, Roberto, Fernández, Felicdad Fernández, Costa, Fabrizio, Velasco, Riccardo, Cestaro, Alessandro, and Sargent, Daniel James
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SINGLE nucleotide polymorphisms ,APPLE genetics ,POLYPLOIDY in plant chromosomes ,PLANT genomes ,AGRONOMY ,MICROARRAY technology ,ROOTSTOCKS - Abstract
High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the ‘Golden Delicious’ genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies. [ABSTRACT FROM AUTHOR]
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- 2013
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10. Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16.
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Khan, Sabaz Ali, Chibon, Pierre-Yves, de Vos, Ric C.H., Schipper, Bert A., Walraven, Evert, Beekwilder, Jules, van Dijk, Thijs, Finkers, Richard, Visser, Richard G.F., van de Weg, Eric W., Bovy, Arnaud, Cestaro, Alessandro, Velasco, Riccardo, Jacobsen, Evert, and Schouten, Henk J.
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GENETICS ,METABOLITES ,APPLES ,ROSACEAE ,PHENOLS - Abstract
Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F1 population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography–mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL®. A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural gene leucoanthocyanidin reductase (LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species. [ABSTRACT FROM PUBLISHER]
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- 2012
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11. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family.
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Illa, Eudald, Sargent, Daniel J., Girona, Elena Lopez, Bushakra, Jill, Cestaro, Alessandro, Crowhurst, Ross, Pindo, Massimo, Cabrera, Antonio, van der Knaap, Esther, Iezzoni, Amy, Gardiner, Susan, Velasco, Riccardo, Arús, Pere, Chagné, David, and Troggio, Michela
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GENOMES ,GENETICS ,MOLECULAR genetics ,GENE mapping ,PRUNUS - Abstract
Background: Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results: We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions: A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae. [ABSTRACT FROM AUTHOR]
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- 2011
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12. Characterization of 25 full-length S-RNase alleles, including flanking regions, from a pool of resequenced apple cultivars
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Luca Dondini, Alessandro Cestaro, Riccardo Velasco, Luca Bianco, Paolo De Franceschi, De Franceschi, Paolo, Bianco, Luca, Cestaro, Alessandro, Dondini, Luca, and Velasco, Riccardo
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0106 biological sciences ,0301 basic medicine ,Malus ,5' Flanking Region ,Apple genome ,Sequence assembly ,Sequence alignment ,Plant Science ,Biology ,01 natural sciences ,Genome ,Self-incompatibility ,Ribonuclease ,Self-Incompatibility in Flowering Plant ,03 medical and health sciences ,Ribonucleases ,Genetic ,S-genotyping ,Genetics ,Coding region ,3' Flanking Region ,Allele ,S-locus ,Promoter Regions, Genetic ,S-locu ,Alleles ,Phylogeny ,Haplotype ,food and beverages ,Self-Incompatibility in Flowering Plants ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Malu ,030104 developmental biology ,Settore AGR/03 - ARBORICOLTURA GENERALE E COLTIVAZIONI ARBOREE ,Agronomy and Crop Science ,Sequence Alignment ,Genome, Plant ,010606 plant biology & botany ,Reference genome - Abstract
Data obtained from Illumina resequencing of 63 apple cultivars were used to obtain full-length S-RNase sequences using a strategy based on both alignment and de novo assembly of reads. The reproductive biology of apple is regulated by the S-RNase-based gametophytic self-incompatibility system, that is genetically controlled by the single, multi-genic and multi-allelic S locus. Resequencing of apple cultivars provided a huge amount of genetic data, that can be aligned to the reference genome in order to characterize variation to a genome-wide level. However, this approach is not immediately adaptable to the S-locus, due to some peculiar features such as the high degree of polymorphism, lack of colinearity between haplotypes and extensive presence of repetitive elements. In this study we describe a dedicated procedure aimed at characterizing S-RNase alleles from resequenced cultivars. The S-genotype of 63 apple accessions is reported; the full length coding sequence was determined for the 25 S-RNase alleles present in the 63 resequenced cultivars; these included 10 previously incomplete sequences (S 5 , S 6a , S 6b , S 8 , S 11 , S 23 , S 39 , S 46 , S 50 and S 58 ). Moreover, sequence divergence clearly suggests that alleles S 6a and S 6b , proposed to be neutral variants of the same alleles, should be instead considered different specificities. The promoter sequences have also been analyzed, highlighting regions of homology conserved among all the alleles.
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- 2018
13. Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum
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Emanuela Coller, Silvio C. E. Tosatto, Lisa Zoli, Elena Baraldi, Alessandro Cestaro, Barbara Zambelli, Baraldi, Elena, Coller, Emanuela, Zoli, Lisa, Cestaro, Alessandro, C E Tosatto, Silvio, and Zambelli, Barbara
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Settore BIO/04 - FISIOLOGIA VEGETALE ,Intrinsically disordered proteins · Plant biotic stress · Strawberry · Colletotrichum acutatum ,Plant biotic stress ,Colletotrichum acutatum ,Plant Science ,Genes, Plant ,Intrinsically disordered proteins ,Fragaria ,Strawberry ,Woodland Strawberry ,Botany ,Colletotrichum ,Genetics ,Plant defense against herbivory ,Agronomy and Crop Science ,Medicine (all) ,Oligonucleotide Array Sequence Analysis ,Plant Diseases ,Plant Proteins ,biology ,food and beverages ,General Medicine ,biology.organism_classification ,Protein tertiary structure ,Host-Pathogen Interactions ,Proteome - Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack secondary and/or tertiary structure under physiological conditions. These proteins are very abun- dant in eukaryotic proteomes and play crucial roles in all molecular mechanisms underlying the response to envi- ronmental challenges. In plants, different IDPs involved in stress response have been identified and characterized. Nevertheless, a comprehensive evaluation of protein dis- order in plant proteomes under abiotic or biotic stresses is not available so far. In the present work the transcriptome dataset of strawberry (Fragaria x ananassa) fruits interact- ing with the fungal pathogen Colletotrichum acutatum was actualized onto the woodland strawberry (Fragaria vesca) genome. The obtained cDNA sequences were translated into protein sequences, which were subsequently subjected to disorder analysis. The results, providing the first estima- tion of disorder abundance associated to plant infection, showed that the proteome activated in the strawberry red fruit during the active fungal propagation is remarkably depleted in disorder. On the other hand, in the resistant Electronic supplementary material The online version of this article (doi:10.1007/s11103-015-0353-7) contains supplementary material, which is available to authorized users. * Barbara Zambelli barbara.zambelli@unibo.it 1 Department of Agricultural Sciences, University of Bologna, Bologna, Italy 2 Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all’ Adige, Trento, Italy 3 Department of Biomedical Sciences, University of Padova, Padua, Italy 4 Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy white fruit, no significant disorder reduction is observed in the proteins expressed in response to fungal infection. Four representative proteins, FvSMP, FvPRKRIP, FvPCD-4 and FvFAM32A-like, predicted as mainly disordered and never experimentally characterized before, were isolated, and the absence of structure was validated at the secondary and tertiary level using circular dichroism and differential scanning fluorimetry. Their quaternary structure was also established using light scattering. The results are discussed considering the role of protein disorder in plant defense.
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- 2015
14. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
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Luca Bianco, Eric van de Weg, Sophia Derdak, Elisa Banchi, Ivo Gut, Daniel J. Sargent, David Chagné, Michela Troggio, Johannes Jansen, Alessandro Cestaro, Mario Di Guardo, François Laurens, Silvio Salvi, Riccardo Velasco, Roberto Viola, Troggio, Michela, Research and Innovation Centre, Edmund Mach Foundation (FEM), Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Wageningen UR Plant Breeding, Wageningen University and Research Centre [Wageningen] (WUR), DipSA, Università di Bologna [Bologna] (UNIBO), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Plant & Food Research, Palmerston North Research Centre, EU seventh Framework Programme by the FruitBreedomics project - Grant Number 265582, Wageningen University and Research [Wageningen] (WUR), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Bianco, Luca, Cestaro, Alessandro, Sargent, Daniel Jame, Banchi, Elisa, Derdak, Sophia, Di Guardo, Mario, Salvi, Silvio, Jansen, Johanne, Viola, Roberto, Gut, Ivo, Laurens, Francoi, Chagné, David, Velasco, Riccardo, and Van De Weg, Eric
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0106 biological sciences ,Genetics and Molecular Biology (all) ,cartographie génomique ,Molecular biology ,Agricultural Biotechnology ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,Genome-wide association study ,variation allélique ,Molecular Inversion Probe ,Computational Biology ,Genetic Markers ,Genotype ,High-Throughput Nucleotide Sequencing ,Malus ,Reproducibility of Results ,Genome, Plant ,Genome-Wide Association Study ,Genomics ,Polymorphism, Single Nucleotide ,Biochemistry, Genetics and Molecular Biology (all) ,Agricultural and Biological Sciences (all) ,01 natural sciences ,Biochemistry ,Laboratorium voor Plantenveredeling ,Sequencing techniques ,Sequence alignment ,Genetic Marker ,Plant Genomics ,Genome Sequencing ,lcsh:Science ,accurate ,Genetics ,malus domestica ,0303 health sciences ,Multidisciplinary ,Genome ,Medicine (all) ,Sequence analysis ,alignment ,Agriculture ,Single Nucleotide ,Tag SNP ,Marker-assisted selection ,PE&RC ,SNP genotyping ,Malu ,Settore AGR/07 - GENETICA AGRARIA ,pomme ,Biometris ,SNP array ,Research Article ,Biotechnology ,construction ,polymorphisme nucléotidique simple (SNP) ,Reproducibility of Result ,Single-nucleotide polymorphism ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,malus micromalus ,analyse de génome ,cultivars ,Polymorphism ,DNA sequence analysis ,030304 developmental biology ,Evolutionary Biology ,Molecular Biology Assays and Analysis Techniques ,Sequence Assembly Tools ,Biology and life sciences ,sélection artificielle ,lcsh:R ,barley ,matériel génétique ,Plant ,Genome Analysis ,linkage map ,High Throughput Screening ,Plant Breeding ,Molecular biology techniques ,Genomic ,Genetic Polymorphism ,lcsh:Q ,Plant Biotechnology ,Population Genetics ,010606 plant biology & botany - Abstract
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina lnfinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus x domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocics and selected up to 11 entries within narrow genomic regions of 5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included similar to 3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where similar to 15.8 K SNP markers were mapped with an average of similar to 6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
- Published
- 2014
15. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin
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Michela Troggio, Felicdad Fernández Fernández, Marco Moretto, Fabrizio Costa, Lara Giongo, Riccardo Velasco, Alessandro Cestaro, Elisa Banchi, Daniel J. Sargent, Luca Bianco, Roberto Viola, Nada Šurbanovski, Troggio, Michela, Šurbanovski, Nada, Bianco, Luca, Moretto, Marco, Giongo, Lara, Banchi, Elisa, Viola, Roberto, Fernández, Felicdad Fernández, Costa, Fabrizio, Velasco, Riccardo, Cestaro, Alessandro, and Sargent, Daniel James
- Subjects
Genetics and Molecular Biology (all) ,Genetic Linkage ,Agricultural Biotechnology ,lcsh:Medicine ,Genome-wide association study ,Plant Science ,Plant Genetics ,Genome ,Biochemistry ,Ploidy ,Plant Genomics ,Genome Sequencing ,lcsh:Science ,Oligonucleotide Array Sequence Analysis ,Genetics ,Multidisciplinary ,Medicine (all) ,Chromosome Mapping ,Agriculture ,Genomics ,Plants ,Settore AGR/07 - GENETICA AGRARIA ,Malus ,Genome, Plant ,Research Article ,Biotechnology ,Marker-Assisted Selection ,Genotype ,Sequence analysis ,Quantitative Trait Loci ,Crops ,Computational biology ,Biology ,Quantitative trait locus ,Genes, Plant ,Polymorphism, Single Nucleotide ,Polyploidy ,Molecular Genetics ,Genetic linkage ,Agricultural and Biological Sciences (all) ,Biochemistry, Genetics and Molecular Biology (all) ,Genotyping ,Genetic association ,Whole genome sequencing ,Population Biology ,lcsh:R ,Botany ,Computational Biology ,Genetic Polymorphism ,Plant Biotechnology ,Structural Genomics ,lcsh:Q ,Population Genetics ,Genome-Wide Association Study - Abstract
High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the ‘Golden Delicious’ genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies.
- Published
- 2013
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