Improving transcriptome de novo assembly by using a reference genome of a related species: translational genomics from oil palm to coconut

Armero Villanueva Alix Augusto, Bocs Stéphanie, Baudouin Luc, This Dominique. 2015. Improving transcriptome de novo assembly by using a reference genome of a related species: translational genomics from oil palm to coconut. In : Plant Genome Evolution 2015. Elsevier. Amsterdam : Elsevier, 1 p. Plant Genome Evolution, Amsterdam, Pays-Bas, 6 Septembre 2015/8 Septembre 2015.

Matériel d'accompagnement : 1 résumé de poster

Résumé : Transcriptome sequencing by next-generation techniques has allowed expanding knowledge of genomics in nonmodel organisms. However, when the transcripts identified by these techniques are compared against the transcripts references (model organisms), there is a high variability in the percentage of recovered transcripts resulting from several biological and technical factors. In this work we propose a methodology that improved the results of de novo assembly of coconut - our species of interest - by using a reference genome (oil palm), thereby ensuring the subjacent biological relevance of results. Two critical stages were evaluated: the identification of novel transcripts and/or exons and the translation of the transcript into amino acid sequences. Two existing approaches (BRANCH and Cufflinks RABT) were used for identifying new transcripts and/or exons, not found by de novo assembly, using the genes of a related species, the raw data of the transcriptome (reads) and transcripts obtained by de novo assembly. In the translation stage a pipeline based on a statistical model that discriminates coding regions, FrameDP, was assessed. The biological pertinence of these two stages was evaluated through a functional analysis. The two approaches identified more than 70000 new transcripts and exons in Cocos nucifera representing an increase of 35% in relation to the initial amount. Over 96% of these new sequences had significant alignments against Uniprot database. A more detailed functional analysis revealed specific features of these new transcripts and exons, compared to those obtained from de novo assembly. The translation pipeline defined protein sequences for 56% of new transcripts. The quality of the protein sequences was confirmed by a significant improvement in the identification of biological functions. Finally, these annotated sequences were used for a comparative analysis in palms. Our methodology allows a more comprehensive representation of the gene space of nonmodel organisms, prior to comparative genomics.

Mots-clés libres : Comparative genomics, Functional analysis, Cocos nucifera, Nonmodel organisms

Classification Agris : F30 - Génétique et amélioration des plantes

Auteurs et affiliations

• Armero Villanueva Alix Augusto, CIRAD-BIOS-UMR AGAP (FRA)
• Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
• Baudouin Luc, CIRAD-BIOS-UMR AGAP (FRA)
• This Dominique, Montpellier SupAgro (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/580121/)

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