De novo assembly of maritime pine transcriptome Implications for forest breeding and biotechnology

Autor: Javier Canales, Christophe Klopp, Marina Rueda-López, Hicham Benzekri, Luc Harvengt, Darío Guerrero-Fernández, Pedro Seoane, Grégoire Le Provost, Rafael A. Cañas, Céline Noirot, Concepción Ávila, Francisco M. Cánovas, Marie-Anne Lelu-Walter, Vanessa Castro-Rodríguez, Francisco R. Cantón, Philippe Label, Rocío Bautista, M. Gonzalo Claros, François Ehrenmann, Caroline Teyssier, Isabelle Lesur, Andreia S. Rodrigues, Josefa Gómez-Maldonado, María Teresa Cervera, Alexandre Morel, Céline Lalanne, Noe Fernandez-Pozo, Célia Miguel, María Angeles Guevara, Christophe Plomion, Jean-François Trontin, Isabelle Reymond, Angel García-Gutiérrez
Přispěvatelé: Universidad de Málaga [Málaga] = University of Málaga [Málaga], Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), HelixVenture, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Instituto de Biologia Experimental e Tecnológica (IBET), Instituto de Technologia Quimica e Biologica, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Plant KBBE programme n°PLE2009-0016 'SUSTAINPINE', Contrat région Centre n°33639 'EMBRYOME'
Jazyk: angličtina
Rok vydání: 2014
Předmět:
DNA
Complementary
[SDV.BIO]Life Sciences [q-bio]/Biotechnology
Genotype
De novo transcriptome assembly
Sequencing data
full-length cDNA
Sequence assembly
Single-nucleotide polymorphism
Plant Science
Computational biology
Breeding
Biology
transcriptome sequencing
Polymorphism
Single Nucleotide
DNA sequencing
Trees
Transcriptome
Genome Size
single nucleotide polymorphism
transcription factors
Databases
Genetic
assemblage du transcriptome
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Translational genomics
Genotyping
Genetics
fungi
High-Throughput Nucleotide Sequencing
food and beverages
Molecular Sequence Annotation
Sequence Analysis
DNA
15. Life on land
Pinus
RNA
Plant
Multigene Family
conifers
next-generation sequencing
Agronomy and Crop Science
Genome
Plant
Microsatellite Repeats
Biotechnology
Zdroj: Repositorio de Resultados de Investigación del INIA
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA
Plant Biotechnology Journal
Plant Biotechnology Journal, 2014, 12 (3), pp.286-299. ⟨10.1111/pbi.12136⟩
Plant Biotechnology Journal, Wiley, 2014, 12 (3), pp.286-299. ⟨10.1111/pbi.12136⟩
INIA: Repositorio de Resultados de Investigación del INIA
ISSN: 1467-7644
1467-7652
Popis: Article fédérateur entre toutes les équipes Européennes travaillant sur le pin maritime. Assemblage du transcriptome des données venant de France (INRA Orléans + INRA Pierroton) + Espagne + Portugal = projet Sustainpine; International audience; Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.
Databáze: OpenAIRE
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