Open AccessDe novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology
Author(s) -
Canales Javier,
Bautista Rocio,
Label Philippe,
GómezMaldonado Josefa,
Lesur Isabelle,
FernándezPozo Noe,
RuedaLópez Marina,
GuerreroFernández Dario,
CastroRodríguez Vanessa,
Benzekri Hicham,
Cañas Rafael A.,
Guevara MaríaAngeles,
Rodrigues Andreia,
Seoane Pedro,
Teyssier Caroline,
Morel Alexandre,
Ehrenmann François,
Provost Grégoire,
Lalanne Céline,
Noirot Céline,
Klopp Christophe,
Reymond Isabelle,
GarcíaGutiérrez Angel,
Trontin JeanFrançois,
LeluWalter MarieAnne,
Miguel Celia,
Cervera María Teresa,
Cantón Francisco R.,
Plomion Christophe,
Harvengt Luc,
Avila Concepción,
Gonzalo Claros M.,
Cánovas Francisco M.
Publication year - 2014
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12136
Subject(s) - biology , transcriptome , sequence assembly , pinus pinaster , de novo transcriptome assembly , computational biology , dna sequencing , gene , ensembl , genetics , genomics , genome , ecology , gene expression
Summary Maritime pine ( P inus pinaster A it.) is a widely distributed conifer species in S outhwestern E urope 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 I llumina. 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 c DNA s. 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 S ustainpine DB , 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.