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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis

Cited 13 times inthomson ciCited 9 times inthomson ci
Title
De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis
Author
Hyun, Tae KyungRim, YeonggilJang, Hui-JeongKim, Cheol HongPark, JongsunKumar, RiteshLee, SunghoonKim, Byung ChulBhak, Jong HwaBinh Nguyen-QuocKim, Seon-WonLee, Sang YeolKim, Jae-Yean
Keywords
Carotenoid; Digital gene expression; Momordica cochinchinensis Spreng; Next generation sequencing; Transcriptome
Issue Date
2012-07
Publisher
SPRINGER
Citation
PLANT MOLECULAR BIOLOGY, v.79, no.4-5, pp.413 - 427
Abstract
The ripe fruit of Momordica cochinchinensis Spreng, known as gac, is featured by very high carotenoid content. Although this plant might be a good resource for carotenoid metabolic engineering, so far, the genes involved in the carotenoid metabolic pathways in gac were unidentified due to lack of genomic information in the public database. In order to expedite the process of gene discovery, we have undertaken Illumina deep sequencing of mRNA prepared from aril of gac fruit. From 51,446,670 high-quality reads, we obtained 81,404 assembled unigenes with average length of 388 base pairs. At the protein level, gac aril transcripts showed about 81.5 % similarity with cucumber proteomes. In addition 17,104 unigenes have been assigned to specific metabolic pathways in Kyoto Encyclopedia of Genes and Genomes, and all of known enzymes involved in terpenoid backbones biosynthetic and carotenoid biosynthetic pathways were also identified in our library. To analyze the relationship between putative carotenoid biosynthesis genes and alteration of carotenoid content during fruit ripening, digital gene expression analysis was performed on three different ripening stages of aril. This study has revealed putative phytoene synthase, 15-cis-phytone desaturase, zeta-carotene desaturase, carotenoid isomerase and lycopene epsilon cyclase might be key factors for controlling carotenoid contents during aril ripening. Taken together, this study has also made availability of a large gene database. This unique information for gac gene discovery would be helpful to facilitate functional studies for improving carotenoid quantities.
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DOI
10.1007/s11103-012-9919-9
ISSN
0167-4412
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BME_Journal Papers
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