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 orde...
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PeerJ Inc.
2017-01-01
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| Online Access: | https://peerj.com/articles/2834.pdf |
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| author | Ah-Young Shin Yong-Min Kim Namjin Koo Su Min Lee Seokhyeon Nahm Suk-Yoon Kwon |
| author_facet | Ah-Young Shin Yong-Min Kim Namjin Koo Su Min Lee Seokhyeon Nahm Suk-Yoon Kwon |
| author_sort | Ah-Young Shin |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T06:59:21Z |
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| id | doaj.art-a65f1a00f42e41ac828040fc96e9d8fc |
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| language | English |
| last_indexed | 2024-03-09T06:59:21Z |
| publishDate | 2017-01-01 |
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| spelling | doaj.art-a65f1a00f42e41ac828040fc96e9d8fc2023-12-03T09:56:54ZengPeerJ Inc.PeerJ2167-83592017-01-015e283410.7717/peerj.2834Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit developmentAh-Young Shin0Yong-Min Kim1Namjin Koo2Su Min Lee3Seokhyeon Nahm4Suk-Yoon Kwon5Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, KoreaKorean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, KoreaKorean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, KoreaR&D Devision, Nongwoo Bio Co., Ltd., Yeoju, Kyonggi-do, KoreaR&D Devision, Nongwoo Bio Co., Ltd., Yeoju, Kyonggi-do, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, KoreaBackground 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.https://peerj.com/articles/2834.pdfKorean melonTranscriptomeFruit developmentPathway analysisSucroseCarotenoids |
| spellingShingle | Ah-Young Shin Yong-Min Kim Namjin Koo Su Min Lee Seokhyeon Nahm Suk-Yoon Kwon Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development PeerJ Korean melon Transcriptome Fruit development Pathway analysis Sucrose Carotenoids |
| 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 | Korean melon Transcriptome Fruit development Pathway analysis Sucrose Carotenoids |
| url | https://peerj.com/articles/2834.pdf |
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