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Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development

BACKGROUND: The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In ord...

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Autores principales: Shin, Ah-Young, Kim, Yong-Min, Koo, Namjin, Lee, Su Min, Nahm, Seokhyeon, Kwon, Suk-Yoon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217523/
https://www.ncbi.nlm.nih.gov/pubmed/28070461
http://dx.doi.org/10.7717/peerj.2834
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author Shin, Ah-Young
Kim, Yong-Min
Koo, Namjin
Lee, Su Min
Nahm, Seokhyeon
Kwon, Suk-Yoon
author_facet Shin, Ah-Young
Kim, Yong-Min
Koo, Namjin
Lee, Su Min
Nahm, Seokhyeon
Kwon, Suk-Yoon
author_sort Shin, Ah-Young
collection PubMed
description BACKGROUND: The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development. RESULTS: We identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs in Arabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation. CONCLUSION: Our results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit.
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spelling pubmed-52175232017-01-09 Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development Shin, Ah-Young Kim, Yong-Min Koo, Namjin Lee, Su Min Nahm, Seokhyeon Kwon, Suk-Yoon PeerJ Agricultural Science BACKGROUND: The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development. RESULTS: We identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs in Arabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation. CONCLUSION: Our results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit. PeerJ Inc. 2017-01-04 /pmc/articles/PMC5217523/ /pubmed/28070461 http://dx.doi.org/10.7717/peerj.2834 Text en ©2017 Shin et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Shin, Ah-Young
Kim, Yong-Min
Koo, Namjin
Lee, Su Min
Nahm, Seokhyeon
Kwon, Suk-Yoon
Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title_full Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title_fullStr Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title_full_unstemmed Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title_short Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development
title_sort transcriptome analysis of the oriental melon (cucumis melo l. var. makuwa) during fruit development
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217523/
https://www.ncbi.nlm.nih.gov/pubmed/28070461
http://dx.doi.org/10.7717/peerj.2834
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