Exploring Flavonoid Biosynthetic Pathway Genes Based on Transcriptome of Ephedra intermedia Germinating Seeds

DENG Nan; SHI Sheng-qing; CHANG Er-mei; LIU Jian-feng; LAN Qian; JIANG Ze-ping

Volume 27 Issue 6

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Exploring Flavonoid Biosynthetic Pathway Genes Based on Transcriptome of Ephedra intermedia Germinating Seeds

1.
Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2014-04-28

Abstract

The application of a new generation high-throughput sequencing technology (Illumina solexa) to global transcriptome of different stages of germinated Ephedra intermedia Schrenk ex Mey seeds showed that 52 007 unigenes were acquired, and the total length was 25 043 596 bp after de novo assembly; among them, 64 751 annotations were from GO, 17 701 from COG and 16 942 from KEGG after functional annotation against these databases; from KEGG pathway, 283 unigenes were associated with flavonoids biosynthetic pathway which contained chalcone synthase, cytochrome, anthocyanidin reductase, etc. The result could provide some references for the study of molecular systematic evolution, utilization of resistance and medicine related genes, and its genetic improvement in the future.
- Ephedra intermedia,
- transcriptome,
- flavonoid,
- high-throughput sequencing

References

[1]	刘媖心. 中国沙漠植物志[M]. 科学出版社, 1985.
[2]	雍世鹏,刘钟龄. 内蒙古植被[Z]. 呼和浩特: 科学出版社, 1985.
[3]	张盹明,杨自辉,王继和,等. 2 种麻黄光合及其耐逆性分析[J]. 西北植物学报. 2007, 27(7): 1473-1478.
[4]	Huang J, Giannasi D E, Price R A. Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences[J]. Molecular Phylogenetics and Evolution. 2005, 35(1): 48-59.
[5]	Price R A. Systematics of the Gnetales: a review of morphological and molecular evidence[J]. International Journal of Plant Sciences. 1996: S40-S49.
[6]	Friedman W E. Double fertilization in Ephedra, a nonflowering seed plant: its bearing on the origin of angiosperms[J]. Science. 1990, 247(4945): 951-954.
[7]	Doyle J A. Seed plant phylogeny and the relationships of Gnetales[J]. International Journal of Plant Sciences. 1996: S3-S39.
[8]	Zhong B, Yonezawa T, Zhong Y, et al. The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics[J]. Molecular Biology and Evolution. 2010, 27(12): 2855-2863.
[9]	查丽杭,苏志国,张国政,等. 麻黄资源的利用与研究开发进展[J]. 植物学通报. 2002, 19(4): 396-405.
[10]	Chen Z, Hu Y, Wu H, et al. Synthesis and biological evaluation of flavonoids as vasorelaxant agents[J]. Bioorganic medicinal chemistry letters. 2004, 14(15): 3949-3952.
[11]	王庆彪. 裸子植物的分子系统发育及麻黄碱类化学成分的进化起源[D]. 复旦大学, 2006.
[12]	白可喻,戎郁萍,徐斌. 甘草和麻黄资源的生物多样性价值和保护[J]. 中国农业资源与区划. 2009(4): 64-69.
[13]	赖陈武,刘颖,李艾莲. 麻黄离体培养研究进展[J]. 世界科学技术:中医药现代化. 2003, 5(2): 37-39.
[14]	Gutterman Y. Survival strategies of annual desert plants[M]. Springer, 2002.
[15]	张勇,薛林贵,高天鹏,等. 荒漠植物种子萌发研究进展[J]. 中国沙漠. 2005, 25(1): 106-112.
[16]	李小白,向林,罗洁,等. 转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J]. 中国细胞生物学学报. 2013(05): 720-726.
[17]	Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes[J]. Nature. 2008, 456(7221): 470-476.
[18]	Sultan M, Schulz M H, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome[J]. Science. 2008, 321(5891): 956-960.
[19]	吴琼,孙超,陈士林,等. 转录组学在药用植物研究中的应用[J]. 世界科学技术: 中医药现代化. 2010(3): 457-462.
[20]	Science For Life Laboratory S, Universitet U, Det M O F V, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology. 2011, 29(7): 644-652.
[21]	Ye J, Fang L, Zheng H, et al. WEGO: a web tool for plotting GO annotations[J]. Nucleic Acids Res. 2006, 34(Web Server issue): W293-W297.
[22]	Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets[J]. Nucleic Acids Res. 2012, 40(Database issue): D109-D114.
[23]	周国艳,胡望雄,徐建红,等. 整合多个组学(omics)分析植物代谢产物及其功能[J]. 浙江大学学报(农业与生命科学版). 2013(03): 237-245.
[24]	Niu S H, Li Z X, Yuan H W, et al. Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny[J]. BMC Genomics. 2013, 14: 263.
[25]	Haegeman A, Joseph S, Gheysen G. Analysis of the transcriptome of the root lesion nematode< i > Pratylenchus coffeae generated by 454 sequencing technology[J]. Molecular and Biochemical Parasitology. 2011, 178(1): 7-14.
[26]	Qin Y, Fang H, Tian Q, et al. Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian< i > Dugesia japonica[J]. Genomics. 2011, 97(6): 364-371.
[27]	Schijlen E G, Ric De Vos C H, van Tunen A J, et al. Modification of flavonoid biosynthesis in crop plants[J]. Phytochemistry. 2004, 65(19): 2631-2648.
[28]	Clegg M T, Durbin M L. Flower color variation: a model for the experimental study of evolution[J]. Proc Natl Acad Sci U S A. 2000, 97(13): 7016-7023.
[29]	朱平,王伟,程克棣. 药用植物功能基因[J]. 中国生物工程杂志. 2004, 24(2): 3-8.
[30]	张华峰,王瑛,黄宏文. 黄酮类化合物生物合成途径的进化及其在淫羊藿中的研究展望[J]. 中草药. 2006, 37(11): 1745-1751.
[31]	Kalra S, Puniya B L, Kulshreshtha D, et al. De Novo Transcriptome Sequencing Reveals Important Molecular Networks and Metabolic Pathways of the Plant, Chlorophytum borivilianum[J]. PLoS ONE. 2013, 8(12): e83336.
[32]	刘红亮,郑丽明,刘青青,等. 非模式生物转录组研究[J]. 遗传. 2013(08): 955-970.
[33]	魏利斌,苗红梅,张海洋. 芝麻发育转录组分析[J]. 中国农业科学. 2012, 45(7): 1246-1256.

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Exploring Flavonoid Biosynthetic Pathway Genes Based on Transcriptome of Ephedra intermedia Germinating Seeds

1. Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2014-04-28

Abstract: The application of a new generation high-throughput sequencing technology (Illumina solexa) to global transcriptome of different stages of germinated Ephedra intermedia Schrenk ex Mey seeds showed that 52 007 unigenes were acquired, and the total length was 25 043 596 bp after de novo assembly; among them, 64 751 annotations were from GO, 17 701 from COG and 16 942 from KEGG after functional annotation against these databases; from KEGG pathway, 283 unigenes were associated with flavonoids biosynthetic pathway which contained chalcone synthase, cytochrome, anthocyanidin reductase, etc. The result could provide some references for the study of molecular systematic evolution, utilization of resistance and medicine related genes, and its genetic improvement in the future.

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Reference (33)

[1]	刘媖心. 中国沙漠植物志[M]. 科学出版社, 1985.
[2]	雍世鹏,刘钟龄. 内蒙古植被[Z]. 呼和浩特: 科学出版社, 1985.
[3]	张盹明,杨自辉,王继和,等. 2 种麻黄光合及其耐逆性分析[J]. 西北植物学报. 2007, 27(7): 1473-1478.
[4]	Huang J, Giannasi D E, Price R A. Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences[J]. Molecular Phylogenetics and Evolution. 2005, 35(1): 48-59.
[5]	Price R A. Systematics of the Gnetales: a review of morphological and molecular evidence[J]. International Journal of Plant Sciences. 1996: S40-S49.
[6]	Friedman W E. Double fertilization in Ephedra, a nonflowering seed plant: its bearing on the origin of angiosperms[J]. Science. 1990, 247(4945): 951-954.
[7]	Doyle J A. Seed plant phylogeny and the relationships of Gnetales[J]. International Journal of Plant Sciences. 1996: S3-S39.
[8]	Zhong B, Yonezawa T, Zhong Y, et al. The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics[J]. Molecular Biology and Evolution. 2010, 27(12): 2855-2863.
[9]	查丽杭,苏志国,张国政,等. 麻黄资源的利用与研究开发进展[J]. 植物学通报. 2002, 19(4): 396-405.
[10]	Chen Z, Hu Y, Wu H, et al. Synthesis and biological evaluation of flavonoids as vasorelaxant agents[J]. Bioorganic medicinal chemistry letters. 2004, 14(15): 3949-3952.
[11]	王庆彪. 裸子植物的分子系统发育及麻黄碱类化学成分的进化起源[D]. 复旦大学, 2006.
[12]	白可喻,戎郁萍,徐斌. 甘草和麻黄资源的生物多样性价值和保护[J]. 中国农业资源与区划. 2009(4): 64-69.
[13]	赖陈武,刘颖,李艾莲. 麻黄离体培养研究进展[J]. 世界科学技术:中医药现代化. 2003, 5(2): 37-39.
[14]	Gutterman Y. Survival strategies of annual desert plants[M]. Springer, 2002.
[15]	张勇,薛林贵,高天鹏,等. 荒漠植物种子萌发研究进展[J]. 中国沙漠. 2005, 25(1): 106-112.
[16]	李小白,向林,罗洁,等. 转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J]. 中国细胞生物学学报. 2013(05): 720-726.
[17]	Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes[J]. Nature. 2008, 456(7221): 470-476.
[18]	Sultan M, Schulz M H, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome[J]. Science. 2008, 321(5891): 956-960.
[19]	吴琼,孙超,陈士林,等. 转录组学在药用植物研究中的应用[J]. 世界科学技术: 中医药现代化. 2010(3): 457-462.
[20]	Science For Life Laboratory S, Universitet U, Det M O F V, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology. 2011, 29(7): 644-652.
[21]	Ye J, Fang L, Zheng H, et al. WEGO: a web tool for plotting GO annotations[J]. Nucleic Acids Res. 2006, 34(Web Server issue): W293-W297.
[22]	Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets[J]. Nucleic Acids Res. 2012, 40(Database issue): D109-D114.
[23]	周国艳,胡望雄,徐建红,等. 整合多个组学(omics)分析植物代谢产物及其功能[J]. 浙江大学学报(农业与生命科学版). 2013(03): 237-245.
[24]	Niu S H, Li Z X, Yuan H W, et al. Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny[J]. BMC Genomics. 2013, 14: 263.
[25]	Haegeman A, Joseph S, Gheysen G. Analysis of the transcriptome of the root lesion nematode< i > Pratylenchus coffeae generated by 454 sequencing technology[J]. Molecular and Biochemical Parasitology. 2011, 178(1): 7-14.
[26]	Qin Y, Fang H, Tian Q, et al. Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian< i > Dugesia japonica[J]. Genomics. 2011, 97(6): 364-371.
[27]	Schijlen E G, Ric De Vos C H, van Tunen A J, et al. Modification of flavonoid biosynthesis in crop plants[J]. Phytochemistry. 2004, 65(19): 2631-2648.
[28]	Clegg M T, Durbin M L. Flower color variation: a model for the experimental study of evolution[J]. Proc Natl Acad Sci U S A. 2000, 97(13): 7016-7023.
[29]	朱平,王伟,程克棣. 药用植物功能基因[J]. 中国生物工程杂志. 2004, 24(2): 3-8.
[30]	张华峰,王瑛,黄宏文. 黄酮类化合物生物合成途径的进化及其在淫羊藿中的研究展望[J]. 中草药. 2006, 37(11): 1745-1751.
[31]	Kalra S, Puniya B L, Kulshreshtha D, et al. De Novo Transcriptome Sequencing Reveals Important Molecular Networks and Metabolic Pathways of the Plant, Chlorophytum borivilianum[J]. PLoS ONE. 2013, 8(12): e83336.
[32]	刘红亮,郑丽明,刘青青,等. 非模式生物转录组研究[J]. 遗传. 2013(08): 955-970.
[33]	魏利斌,苗红梅,张海洋. 芝麻发育转录组分析[J]. 中国农业科学. 2012, 45(7): 1246-1256.

Exploring Flavonoid Biosynthetic Pathway Genes Based on Transcriptome of Ephedra intermedia Germinating Seeds

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通讯作者: 陈斌, bchen63@163.com

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Exploring Flavonoid Biosynthetic Pathway Genes Based on Transcriptome of Ephedra intermedia Germinating Seeds

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