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RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by AB...

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Autores principales: Gaete-Eastman, Carlos, Stappung, Yazmina, Molinett, Sebastián, Urbina, Daniela, Moya-Leon, María Alejandra, Herrera, Raúl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9530326/
https://www.ncbi.nlm.nih.gov/pubmed/36204060
http://dx.doi.org/10.3389/fpls.2022.976901
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author Gaete-Eastman, Carlos
Stappung, Yazmina
Molinett, Sebastián
Urbina, Daniela
Moya-Leon, María Alejandra
Herrera, Raúl
author_facet Gaete-Eastman, Carlos
Stappung, Yazmina
Molinett, Sebastián
Urbina, Daniela
Moya-Leon, María Alejandra
Herrera, Raúl
author_sort Gaete-Eastman, Carlos
collection PubMed
description Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by ABA, and a complete set of genes participate in its softening, color, and aroma development. In addition, a set of transcription factors regulate the entire process, but few of them have been described. Over the last two decades, RNA-seq was used to identify genes at three fruit development/ripening stages, named C2 (unripe, large green) to C4 (full ripe), in whole fruit and fruit without achenes. A total of 204,754 contigs were assembled considering all samples, obtaining an N50 of 1.125 bp. Differentially expressed genes (DEGs) between two samples were identified, obtaining a total of 77,181 DEGs. Transcripts for genes involved in ABA biosynthesis present high and differential expression during the C2, C3, and C4 stages. Besides, contigs corresponding to ABA receptors, which interact with a regulatory network, are also differentially expressed. Genes associated with cell wall remodeling and those involved in flavonoid synthesis were also differentially expressed. An interaction network was built considering differentially expressed genes for the phenylpropanoid and flavonoid molecular pathways and having FcMYB1 as a transcription factor regulator. Identifying key genes could give an option to control the ripening of this non-climacteric fruit.
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spelling pubmed-95303262022-10-05 RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit Gaete-Eastman, Carlos Stappung, Yazmina Molinett, Sebastián Urbina, Daniela Moya-Leon, María Alejandra Herrera, Raúl Front Plant Sci Plant Science Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by ABA, and a complete set of genes participate in its softening, color, and aroma development. In addition, a set of transcription factors regulate the entire process, but few of them have been described. Over the last two decades, RNA-seq was used to identify genes at three fruit development/ripening stages, named C2 (unripe, large green) to C4 (full ripe), in whole fruit and fruit without achenes. A total of 204,754 contigs were assembled considering all samples, obtaining an N50 of 1.125 bp. Differentially expressed genes (DEGs) between two samples were identified, obtaining a total of 77,181 DEGs. Transcripts for genes involved in ABA biosynthesis present high and differential expression during the C2, C3, and C4 stages. Besides, contigs corresponding to ABA receptors, which interact with a regulatory network, are also differentially expressed. Genes associated with cell wall remodeling and those involved in flavonoid synthesis were also differentially expressed. An interaction network was built considering differentially expressed genes for the phenylpropanoid and flavonoid molecular pathways and having FcMYB1 as a transcription factor regulator. Identifying key genes could give an option to control the ripening of this non-climacteric fruit. Frontiers Media S.A. 2022-09-20 /pmc/articles/PMC9530326/ /pubmed/36204060 http://dx.doi.org/10.3389/fpls.2022.976901 Text en Copyright © 2022 Gaete-Eastman, Stappung, Molinett, Urbina, Moya-Leon and Herrera. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Gaete-Eastman, Carlos
Stappung, Yazmina
Molinett, Sebastián
Urbina, Daniela
Moya-Leon, María Alejandra
Herrera, Raúl
RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title_full RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title_fullStr RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title_full_unstemmed RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title_short RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit
title_sort rnaseq, transcriptome analysis and identification of degs involved in development and ripening of fragaria chiloensis fruit
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9530326/
https://www.ncbi.nlm.nih.gov/pubmed/36204060
http://dx.doi.org/10.3389/fpls.2022.976901
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