title: Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.
abstract: Next-generation sequencing technologies allow an almost exhaustive survey of the transcriptome, even in species with no available genome sequence. To produce a Unigene set representing most of the expressed genes of pea, 20 cDNA libraries produced from various plant tissues harvested at various developmental stages from plants grown under contrasting nitrogen conditions were sequenced. Around one billion reads and 100 Gb of sequence were de novo assembled. Following several steps of redundancy reduction, 46 099 contigs with N50 length of 1667 nt were identified. These constitute the 'Caméor' Unigene set. The high depth of sequencing allowed identification of rare transcripts and detected expression for approximately 80% of contigs in each library. The Unigene set is now available online (http://bios.dijon.inra.fr/FATAL/cgi/pscam.cgi), allowing (i) searches for pea orthologs of candidate genes based on gene sequences from other species, or based on annotation, (ii) determination of transcript expression patterns using various metrics, (iii) identification of uncharacterized genes with interesting patterns of expression, and (iv) comparison of gene ontology pathways between tissues. This resource has allowed identification of the pea orthologs of major nodulation genes characterized in recent years in model species, as a major step towards deciphering unresolved pea nodulation phenotypes. In addition to a remarkable conservation of the early transcriptome nodulation apparatus between pea and Medicago truncatula, some specific features were highlighted. The resource provides a reference for the pea exome, and will facilitate transcriptome and proteome approaches as well as SNP discovery in pea.
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Susete
authors: S
authors: Alves-Carvalho
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Grégoire
authors: G
authors: Aubert
authors: Laboratoire des Interactions Plantes Micro-Organismes, Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, 24 chemin de Borde Rouge, 31326, Castanet Tolosan, France.
authors: Sébastien
authors: S
authors: Carrère
authors: GENOSCOPE, 2 Rue Gaston Crémieux, 91000, Evry, France.
authors: Corinne
authors: C
authors: Cruaud
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Anne-Lise
authors: AL
authors: Brochot
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Françoise
authors: F
authors: Jacquin
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Anthony
authors: A
authors: Klein
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Chantal
authors: C
authors: Martin
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Karen
authors: K
authors: Boucherot
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Jonathan
authors: J
authors: Kreplak
authors: GENOSCOPE, 2 Rue Gaston Crémieux, 91000, Evry, France.
authors: Corinne
authors: C
authors: da Silva
authors: Laboratoire des Interactions Plantes Micro-Organismes, Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, 24 chemin de Borde Rouge, 31326, Castanet Tolosan, France.
authors: Sandra
authors: S
authors: Moreau
authors: Laboratoire des Interactions Plantes Micro-Organismes, Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, 24 chemin de Borde Rouge, 31326, Castanet Tolosan, France.
authors: Pascal
authors: P
authors: Gamas
authors: GENOSCOPE, 2 Rue Gaston Crémieux, 91000, Evry, France.
authors: Patrick
authors: P
authors: Wincker
authors: Laboratoire des Interactions Plantes Micro-Organismes, Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, 24 chemin de Borde Rouge, 31326, Castanet Tolosan, France.
authors: Jérôme
authors: J
authors: Gouzy
authors: Institut National de la Recherche Agronomique, UMR1347, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France.
authors: Judith
authors: J
authors: Burstin
mesh_terms: D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D018532:Pisum sativum / Q000235:genetics* / Q000254:growth & development*; D055170:Plant Root Nodulation / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development*; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D018749:RNA, Plant
keywords: Pisum sativum L.; de novo assembly; gene expression atlas; next-generation sequencing; nitrogen symbiotic fixation; nodule development