title: De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology.
abstract: 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.
authors.affiliation: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Canales
authors.forename: Rocio
authors.initials: R
authors.lastname: Bautista
authors.forename: Philippe
authors.initials: P
authors.lastname: Label
authors.forename: Josefa
authors.initials: J
authors.lastname: Gómez-Maldonado
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lesur
authors.forename: Noe
authors.initials: N
authors.lastname: Fernández-Pozo
authors.forename: Marina
authors.initials: M
authors.lastname: Rueda-López
authors.forename: Dario
authors.initials: D
authors.lastname: Guerrero-Fernández
authors.forename: Vanessa
authors.initials: V
authors.lastname: Castro-Rodríguez
authors.forename: Hicham
authors.initials: H
authors.lastname: Benzekri
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Cañas
authors.forename: María-Angeles
authors.initials: MA
authors.lastname: Guevara
authors.forename: Andreia
authors.initials: A
authors.lastname: Rodrigues
authors.forename: Pedro
authors.initials: P
authors.lastname: Seoane
authors.forename: Caroline
authors.initials: C
authors.lastname: Teyssier
authors.forename: Alexandre
authors.initials: A
authors.lastname: Morel
authors.forename: François
authors.initials: F
authors.lastname: Ehrenmann
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
authors.forename: Céline
authors.initials: C
authors.lastname: Lalanne
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: Isabelle
authors.initials: I
authors.lastname: Reymond
authors.forename: Angel
authors.initials: A
authors.lastname: García-Gutiérrez
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Trontin
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Lelu-Walter
authors.forename: Celia
authors.initials: C
authors.lastname: Miguel
authors.forename: María Teresa
authors.initials: MT
authors.lastname: Cervera
authors.forename: Francisco R
authors.initials: FR
authors.lastname: Cantón
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.forename: Luc
authors.initials: L
authors.lastname: Harvengt
authors.forename: Concepción
authors.initials: C
authors.lastname: Avila
authors.forename: M
authors.initials: M
authors.lastname: Gonzalo Claros
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Cánovas
mesh_terms: D001709:Biotechnology; D001947:Breeding; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D059646:Genome Size; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D028223:Pinus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome; D014197:Trees
chemical_list: D018076:DNA, Complementary; D018749:RNA, Plant; D014157:Transcription Factors
keywords: conifers; full-length cDNA; next-generation sequencing; single nucleotide polymorphism; transcription factors; transcriptome sequencing