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Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds

Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a hig...

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Detalles Bibliográficos
Autores principales: Darnet, Elaine, Teixeira, Bruno, Schaller, Hubert, Rogez, Hervé, Darnet, Sylvain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10253617/
https://www.ncbi.nlm.nih.gov/pubmed/37298279
http://dx.doi.org/10.3390/ijms24119315
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author Darnet, Elaine
Teixeira, Bruno
Schaller, Hubert
Rogez, Hervé
Darnet, Sylvain
author_facet Darnet, Elaine
Teixeira, Bruno
Schaller, Hubert
Rogez, Hervé
Darnet, Sylvain
author_sort Darnet, Elaine
collection PubMed
description Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model.
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spelling pubmed-102536172023-06-10 Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds Darnet, Elaine Teixeira, Bruno Schaller, Hubert Rogez, Hervé Darnet, Sylvain Int J Mol Sci Article Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model. MDPI 2023-05-26 /pmc/articles/PMC10253617/ /pubmed/37298279 http://dx.doi.org/10.3390/ijms24119315 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Darnet, Elaine
Teixeira, Bruno
Schaller, Hubert
Rogez, Hervé
Darnet, Sylvain
Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title_full Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title_fullStr Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title_full_unstemmed Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title_short Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds
title_sort elucidating the mesocarp drupe transcriptome of açai (euterpe oleracea mart.): an amazonian tree palm producer of bioactive compounds
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10253617/
https://www.ncbi.nlm.nih.gov/pubmed/37298279
http://dx.doi.org/10.3390/ijms24119315
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