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

被引:61
作者
Hyun, Tae Kyung [1 ]
Rim, Yeonggil [1 ]
Jang, Hui-Jeong [1 ]
Kim, Cheol Hong [2 ]
Park, Jongsun [2 ]
Kumar, Ritesh [1 ]
Lee, Sunghoon [2 ]
Kim, Byung Chul [2 ]
Bhak, Jong [2 ]
Binh Nguyen-Quoc [3 ]
Kim, Seon-Won [1 ]
Lee, Sang Yeol [1 ]
Kim, Jae-Yean [1 ]
机构
[1] Gyeongsang Natl Univ, Div Appl Life Sci, WCU Program BK21, Plant Mol Biol & Biotechnol Res Ctr, Jinju 660701, South Korea
[2] Theragen Bio Inst, Suwon 443766, South Korea
[3] Biotechnol Ctr Hochiminh City, Ho Chi Minh City, Vietnam
关键词
Carotenoid; Digital gene expression; Momordica cochinchinensis Spreng; Next generation sequencing; Transcriptome; ISOPRENOID BIOSYNTHESIS; BETA-CAROTENE; EARLY STEPS; RNA-SEQ; EXPRESSION; LYCOPENE; IDENTIFICATION; INVERTASE; SYNTHASE; PLANTS;
D O I
10.1007/s11103-012-9919-9
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:413 / 427
页数:15
相关论文
共 72 条
  • [1] De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques
    Angeloni, F.
    Wagemaker, C. A. M.
    Jetten, M. S. M.
    den Camp, H. J. M. Op
    Janssen-Megens, E. M.
    Francoijs, K-J
    Stunnenberg, H. G.
    Ouborg, N. J.
    [J]. MOLECULAR ECOLOGY RESOURCES, 2011, 11 (04) : 662 - 674
  • [2] [Anonymous], 2001, Acids Res, DOI DOI 10.1093/NAR/29.22.4633
  • [3] Carotenoid pigments in GAC fruit (Momordica cochinchinensis SPRENG)
    Aoki, H
    Kieu, NTM
    Kuze, N
    Tomisaka, K
    Van Chuyen, N
    [J]. BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 2002, 66 (11) : 2479 - 2482
  • [4] The significance of digital gene expression profiles
    Audic, S
    Claverie, JM
    [J]. GENOME RESEARCH, 1997, 7 (10): : 986 - 995
  • [5] Benjamini Y, 2001, ANN STAT, V29, P1165
  • [6] The evolution of supertrees
    Bininda-Emonds, ORP
    [J]. TRENDS IN ECOLOGY & EVOLUTION, 2004, 19 (06) : 315 - 322
  • [7] Regulation of carotenoid formation during tomato fruit ripening and development
    Bramley, PM
    [J]. JOURNAL OF EXPERIMENTAL BOTANY, 2002, 53 (377) : 2107 - 2113
  • [8] Burke D. S., 2005, Current Topics in Nutraceutical Research, V3, P259
  • [9] Busch M, 2002, PLANT PHYSIOL, V128, P439, DOI 10.1104/pp.010573
  • [10] A putative plastidic glucose translocator is expressed in heterotrophic tissues that do not contain starch, during olive (Olea europea L.) fruit ripening
    Butowt, R
    Granot, D
    Rodríguez-García, MI
    [J]. PLANT AND CELL PHYSIOLOGY, 2003, 44 (11) : 1152 - 1161