Data from: Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing PhyloH as a novel phylogenetic diversity analysis toolAnna Sandionigi, Saverio Vicario, Erica M. Prosdocimi, Andrea Galimberti, Emanuele Ferri, Antonia Bruno, Bachir Balech, Valerio Mezzasalma & Maurizio Casiraghi
The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with...
Data from: Molecular and morphological diversity of on-farm hazelnut (Corylus avellana L.) landraces from southern Europe and their role in the origin and diffusion of cultivated germplasmP. Boccacci, M. Aramini, N. Valentini, L. Bacchetta, M. Rovira, P. Drogoudi, A. P. Silva, A. Solar, F. Calizzano, V. Erdoğan, V. Cristofori, L. F. Ciarmiello, C. Contessa, J. J. Ferreira, F. P. Marra & R. Botta
Hazelnut (Corylus avellana L.) is a traditional nut crop in southern Europe. Germplasm exploration conducted on-farm in five countries (Portugal, Spain, Italy, Slovenia, and Greece) identified 77 landraces. The present work describes phenotypic variation in nut and husk traits and investigates genetic relationships using 10 simple sequence repeat (SSR) markers among these landraces, 57 well-known references cultivars, and 19 wild accessions. Among the 77 landraces, 42 had unique fingerprints while 35 showed a SSR profile...
Data from: Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine developmentMaria Concetta Palumbo, Sara Zenoni, Marianna Fasoli, Mélanie Massonnet, Lorenzo Farina, Filippo Castiglione, Mario Pezzotti & Paola Paci
We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named “fight-club hubs” characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named “switch...
Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseqMarie-Joe Karam, François Lefèvre, Magda Bou Dagher-Kharrat, Sara Pinosio & Giovanni Vendramin
We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina® reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script...
Data from: First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill.Sara Pinosio, Santiago C. González-Martínez, Francesca Bagnoli, Federica Cattonaro, Delphine Grivet, Fabio Marroni, Zaida Lorenzo, Juli G. Pausas, Miguel Verdú & Giovanni G. Vendramin
Pinus halepensis is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. Deciphering the molecular basis of Aleppo pine to the Mediterranean environment is therefore needed. In this study we performed Illumina next-generation sequencing of two phenotypically divergent Pinus halepensis accessions with the aims of i) characterizing the transcriptome through Illumina RNA-Seq of two accessions, phenotypically divergent for adaptive traits link to fire adaptation and drought, ii)...
National Research Council5
Institute of Biosciences and Bioresources2
University of Milan1
Institute for Research and Technology in Food and Agriculture1
University of Lausanne1
University of Milano-Bicocca1
National Agency For New Technologies, Energy and Sustainable Economic Development1
Sapienza University of Rome1
Spanish National Research Council1