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

Summary 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.

Transcriptomic Studies in Non-Model Plants: Case of Pisum sativum L. and Medicago lupulina L.

“…Alves-Carvalho et al [39] sequenced transcriptomes of roots, nodules, shoots, leaves, lowers, seeds, tendrils and pods harvested at diferent developmental stages of pea cultivar 'Caméor'. Sequencing of 20 cDNA libraries produced one billion reads.…”

“…Analysis of diferential expression of these genes revealed a negative correlation between soluble sugar and starch lux in vegetable and grain pea seeds [32]. Alves-Carvalho et al [39] developed the Pea RNA-Seq gene atlas containing expression proiles of thousands of genes in diferent pea tissues harvested at distinct developmental stages [48].…”

“…viciae RCAM1026 [51]. All the obtained reads were sequentially mapped to the RCAM1026 genome (about 8% mapped reads), then to the pea transcriptome assembly from Alves-Carvalho et al [39] (about 60% mapped reads) resulting in two sets of differential transcriptome data. The transcript quantiication was carried out using the edgeR package [52].…”

The evolution of determinate and indeterminate nodules within the Papilionoideae subfamily

“…These are the model systems Lotus japonicus (Lotus) and Medicago truncatula (Medicago). Further, some legume crops have been studied in some detail, examples are soybean, pea, and clover (Schmutz et al, 2010;Smykal et al, 2014;Zhukov et al, 2015;Alves-Carvalho et al, 2015;Webb et al, 2014). However, none of these legume species is adapted to severe environmental stress conditions, whereas many other legumes have this ability, including for example Indigofera spp., Mimosa spp.…”

PLANT DEFENSINS: BIOLOGICAL FUNCTION, MECHANISMS OF ACTION AND METHODS OF ANALYSIS (review)

“…Thus, using the expression atlases, it becomes possible to identify the expression profile of certain groups of genes. This allows us to estimate the organ or tissue specificity of the expression of a particular gene and its involvement in certain processes [63,64].…”