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Full‐length de novo assembly of RNA‐seq data in pea ( P isum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species
Author(s) -
AlvesCarvalho Susete,
Aubert Grégoire,
Carrère Sébastien,
Cruaud Corinne,
Brochot AnneLise,
Jacquin Françoise,
Klein Anthony,
Martin Chantal,
Boucherot Karen,
Kreplak Jonathan,
Silva Corinne,
Moreau Sandra,
Gamas Pascal,
Wincker Patrick,
Gouzy Jérôme,
Burstin Judith
Publication year - 2015
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12967
Subject(s) - unigene , biology , de novo transcriptome assembly , sequence assembly , transcriptome , medicago truncatula , gene , genetics , expressed sequence tag , computational biology , rna seq , contig , genome , nanopore sequencing , gene expression , symbiosis , bacteria
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.