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

Javier Canales, Rocio Bautista, Philippe Label, Josefa Gómez-Maldonado, Isabelle Lesur, Noe Fernández-Pozo, Marina Rueda-López, Dario Guerrero-Fernández, Vanessa Castro-Rodríguez, Hicham Benzekri, Rafael A. Cañas, María Angeles Guevara, Andreia Rodrigues, Pedro Seoane, Caroline Teyssier, Alexandre Morel, François Ehrenmann, Grégoire Le Provost, Céline Lalanne, Céline NoirotChristophe Klopp, Isabelle Reymond, Angel García-Gutiérrez, Jean François Trontin, Marie Anne Lelu-Walter, Celia Miguel, María Teresa Cervera, Francisco R. Cantón, Christophe Plomion, Luc Harvengt, Concepción Avila, M. Gonzalo Claros, Francisco M. Cánovas

Research output: Contribution to journalArticlepeer-review

77 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)286-299
Number of pages14
JournalPlant Biotechnology Journal
Volume12
Issue number3
DOIs
Publication statusPublished - 2014

Keywords

  • Conifers
  • Full-length cDNA
  • Next-generation sequencing
  • Single nucleotide polymorphism
  • Transcription factors
  • Transcriptome sequencing

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