title: De novo construction of a "Gene-space" for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources.
abstract: BACKGROUND
  The continuing increase in size and quality of the "short reads" raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a significant challenge due to the large number of repeated sequences which are problematic for a whole-genome quality de novo assembly. Furthermore, for most SNP identification approaches in plant genetics and breeding, only the "Gene-space" regions including the promoter, exon and intron sequences are considered.
  
  
  RESULTS
  We developed the iPea protocol to produce a de novo Gene-space assembly by reconstructing, in an iterative way, the non-coding sequence flanking the Unigene cDNA sequence through addition of next-generation DNA-seq data. The approach was elaborated with the large diploid genome of pea (Pisum sativum L.), rich in repetitive sequences. The final Gene-space assembly included 35,400 contigs (97 Mb), covering 88 % of the 40,227 contigs (53.1 Mb) of the PsCam_low-copy Unigen set. Its accuracy was validated by the results of the built GenoPea 13.2 K SNP Array.
  
  
  CONCLUSIONS
  The iPEA protocol allows the reconstruction of a Gene-space based from RNA-Seq and DNA-seq data with limited computing resources.
authors: INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France. christelle.aluome@u-bordeaux.fr.
authors: Christelle
authors: C
authors: Aluome
authors: INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France. gregoire.aubert@dijon.inra.fr.
authors: Grégoire
authors: G
authors: Aubert
authors: INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France. susete.ac@gmail.com.
authors: Susete
authors: S
authors: Alves Carvalho
authors: INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France. le.paslier@cng.fr.
authors: Marie-Christine
authors: MC
authors: Le Paslier
authors: INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France. judith.burstin@dijon.inra.fr.
authors: Judith
authors: J
authors: Burstin
authors: INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France. dominique.brunel@versailles.inra.fr.
authors: Dominique
authors: D
authors: Brunel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004171:Diploidy; D018745:Genome, Plant; D023281:Genomics; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018532:Pisum sativum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results