Baratti M.,National Research Council Italy |
Cattonaro F.,IGA Technology Services Srl |
Di Lorenzo T.,National Research Council Italy |
Galassi D.M.P.,University of L'Aquila |
And 16 more authors.
Molecular Ecology Resources | Year: 2015
This article documents the public availability of (i) RAD sequencing data and validated SNPs for the American mink Neovison vison and (ii) Transcriptome resources for two nonmodel freshwater crustacean species, the copepod Eucyclops serrulatus and the amphipod Echinogammarus veneris. © 2015 John Wiley & Sons Ltd.
Pinosio S.,National Research Council Italy |
Pinosio S.,IGA Technology Services s.r.l. |
Gonzalez-Martinez S.C.,National Institute for Agriculture and Food Research and Technology INIA |
Gonzalez-Martinez S.C.,University of Lausanne |
And 6 more authors.
Molecular Ecology Resources | Year: 2014
Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48 629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34 014 SNPs across species, with a Ka/Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28 236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes. © 2014 John Wiley & Sons Ltd.
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: SFS-07b-2015 | Award Amount: 7.99M | Year: 2016
The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services. To reach its goal, GenTree will make scientific, technological and implementation breakthroughs in: (i) designing innovative strategies for dynamic conservation of FGR in European forests, (ii) broadening the range of FGR used by European breeding programmes, and (iii) preparing new forest management scenarios and policy frameworks fully integrating genetic conservation and breeding aspects, to adapt forests and forestry to changing environmental conditions and societal demands. GenTree focuses on economically and ecologically important tree species in Europe, growing in a wide range of habitats and covering different societal uses and values. The major outputs of GenTree will include: (i) much needed new scientific knowledge on phenotypic and genotypic diversity across environmental gradients in Europe, (ii) improved genotyping and phenotyping monitoring tools for practitioners, (iii) updated and refined data for information systems of in-situ and ex-situ FGR collections, (iv) innovative strategies for conservation, breeding and exchanging and using diversified forest reproductive material, (v) novel outreach and science-policy support tools to better integrate FGR concerns into forest management and better implement relevant international commitments in Europe. GenTree will improve the status and use of European in-situ and ex-situ FGR collections, support acquisition, conservation, characterisation, evaluation and use of relevant FGR in breeding and forestry practice and policy, will seek to harmonise, rationalise and improve management of existing collections and databases, and will strengthen the EU strategy for cooperation on FGR research and innovation.
Agency: Cordis | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.3.1-01 | Award Amount: 11.66M | Year: 2012
The goal of WATBIO is to use the power of next generation sequencing to develop an accelerated route for producing new germplasm with enhanced drought tolerance whilst maintaining biomass productivity and quality in water scarce, marginal environments unsuitable for food crops. This will be achieved for three non-food crops (Populus, Miscanthus and Arundo), suitable for growth on water scarce, marginal lands, through a 5-year translational research project. Populus and Miscanthus germplasm with increased drought tolerance will be produced within WATBIO whilst for Arundo its genetic diversity will be assessed and breeding tools developed. Twenty-two multidisciplinary partners (14 academics, and 7 SMEs) spanning the whole value chain for crop production will collectively achieve this innovation by 1) identifying key molecular, cellular and physiological traits for the maintenance of biomass production, lignocellulosic quality and water use efficiency in water-scarce environments; 2) linking these traits through modelling to underlying key genes, proteins and metabolite networks; 3) utilising a wide range of germplasm for screening in phenotyping platforms and field measurements at multiple sites to test importance of genotype x environment interactions in determining traits; 4) using sequence based gene expression data, identify 40 genes related to drought tolerance for testing proof of concept using GM approach; and 5) using sequence-based data for genome wide association and genetical genomic approaches, link physiology to traits of high heritability and to underlying genes. WATBIO will transfer knowledge of commercial significance using its industrial partners and stakeholders enabling the deployment of biotechnology to boost European competitiveness, without the necessity of GM. Through workshops, seminars and exchanges, WATBIO will train the next generation of multi-disciplinary professionals in the area of biomass crop production on marginal lands.
Yin X.-W.,University of Pisa |
Yin X.-W.,China Agricultural University |
Iovinella I.,University of Pisa |
Marangoni R.,University of Pisa |
And 6 more authors.
Cellular and Molecular Life Sciences | Year: 2013
Solitary bees are major pollinators but their chemical communication system has been poorly studied. We investigated olfactory coding in Osmia cornuta from two perspectives, chemical and biochemical. We identified (E)-geranyl acetone and 2-hexyl-1,3-dioxolane, specifically secreted by females and males, respectively. A transcriptome analysis of antennae revealed 48 ORs (olfactory receptors), six OBPs (odorant-binding proteins), five CSPs (chemosensory proteins), and a single SNMP (sensory neuron membrane protein). The numbers of ORs and OBPs are much lower than in the honeybee, in particular, C-minus OBPs are lacking in the antennae of O. cornuta. We have expressed all six OBPs of O. cornuta and studied their binding specificities. The best ligands are common terpene plant odorants and both volatiles produced by the bee and identified in this work. © 2013 Springer Basel.
Agency: Cordis | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.3.1-01 | Award Amount: 8.64M | Year: 2013
Plant natural products have been utilised by human civilisation for millennia, providing vital medicines and essential dietary components. More recently bioactive compounds from plant sources have been used in cosmetics, as health supplements and are important components of feedstuffs. Despite significant investments new activities and new sustainable biosources are required to alleviate our reliance on chemical synthesis. In the DISCO project we aim to address these issues and create a framework that can act as a generic pipeline capable of taking discovery through application and validation, to translation and industrial valorisation. Key aspects of the project will be concerned with (i) translating discovery into industrial feasibility and/or commercialisation, (ii) transfer our knowledge gained optimising isoprenoid/terpenoid production to other important terpenoids and different classes of natural products, (iii) maintaining and incorporating the very latest technologies into both the discovery and translational pipelines and (iv) develop green factories with integrated biorefining pipelines to reduce or eliminate chemical refining and thus environmental impact. The bioactive molecules and their biochemical pathways targeted include, carotenoids (including apo-carotenoids), terpenoids and tropane alkaloid. For example; ketocarotenoids which are used as colorants in feedstuffs especially aquaculture; colourless carotenes such as phytoene and phytofluene, which are important bioactive ingredients of cosmetics; apo-carotenoids from saffron which are colorants and potent bioactives; the terpenoid solanesol which is used in the production of Coenzyme Q10 and the alkaloid scopolamine which is used as analgesic. The project will have real-life impacts reducing environmental impact, provide new material to benefit human activities and stimulate economic development.
Guiatti D.,University of Udine |
Pomari E.,University of Udine |
Radovic S.,IGA Technology Services Srl |
Spadotto A.,IGA Technology Services Srl |
Stefanon B.,University of Udine
PLoS ONE | Year: 2015
The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus-scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6%mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY1 system confirms that this "human-on-pig" approach offers new potentiality for the identification of DNA variants in protein-coding genes. Copyright: © 2015 Guiatti et al.
PubMed | University of Udine, IGA Technology Services Srl and University of Catanzaro
Type: Journal Article | Journal: Oncotarget | Year: 2016
RNA binding proteins (RBPs) play a central role in cell physiology and pathology. Among them, HuR is a nuclear RBP, which shuttles to the cytoplasm to allow its RNA targets processing. HuR over-expression and delocalization are often associated to cell transformation. Numerous cancers display increased HuR protein levels and its high cytoplasmic levels has been associated with a worse prognosis.In our study, we first evaluated HuR expression in normal and cancer thyroid tissues and then evaluated its function in thyroid cell lines. HuR is over-expressed in all thyroid tumor tissues; high cytoplasmic levels are detected in all thyroid carcinomas. HuR silencing decreased cell viability and determined apoptotic cell death, in a non-tumorigenic (Nthy-ori-3.1) and a tumorigenic (BCPAP) thyroid cell line. Global transcriptome analysis indicated that HuR silencing, though having similar biological effects, induces distinct gene expression modifications in the two cell lines. By using the RIP-seq approach, the HuR-bound RNA profiles of different thyroid cell lines were evaluated. We show that in distinct cell lines HuR-bound RNA profiles are different. A set of 114 HuR-bound RNAs distinguishing tumorigenic cell lines from the non-tumorigenic one was identified.Altogether, our data indicate that HuR plays a role in thyroid tumorigenesis. Moreover, our findings are a proof of concept that RBP targets differ between cells with the same origin but with distinct biological behavior.
PubMed | University of Udine and IGA Technology Services Srl
Type: Journal Article | Journal: PloS one | Year: 2015
The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY system confirms that this human-on-pig approach offers new potentiality for the identification of DNA variants in protein-coding genes.