Comprehensive analysis of Panax ginseng root transcriptomes.
Comprehensive analysis of Panax ginseng root transcriptomes.
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DOI：
10.1186/s12870-015-0527-0
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发表时间：
2015-06-12
影响因子：
5.3
通讯作者：
Yang TJ
中科院分区：
文献类型：
--
作者：
Jayakodi M;Lee SC;Lee YS;Park HS;Kim NH;Jang W;Lee HO;Joh HJ;Yang TJ
高丽参（Panax ginseng C.A.）Meyer）是一种高效的药用植物，含有具有多种药理活性的皂苷，其根被商业化地生产用于生药。在这里，我们使用Illumina平台从四个根样本中生成了超过2.32亿个RNA测序读数，包括来自一年生植物的全根和来自六年生植物的三种类型的根组织（即，主根体、根状茎和侧根）。通过从头组装和参考辅助选择，我们获得了由55，949个平均长度为1，250 bp的转录物组成的非冗余单基因集。在单基因组中的转录物中，94%通过对蛋白质数据库的相似性搜索进行功能注释。大约28.6%的转录本代表了以前没有报道过的人参新基因序列。数字表达谱分析揭示了364个基因在四个根样品中显示出差异表达模式。此外，32个在一年生的根中唯一表达，而7个在六年生的根组织中唯一表达。我们确定了38个转录本编码酶参与β-内酰胺酶的生物合成途径和189编码UDP-糖基转移酶。我们的分析为人参根转录组在发育和次生代谢物生物合成中的作用提供了新的见解。本文的在线版本（doi：10.1186/s12870-015-0527-0）包含补充材料，可供授权用户使用。
Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs. Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases. Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng. The online version of this article (doi:10.1186/s12870-015-0527-0) contains supplementary material, which is available to authorized users.
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影响因子：
12.3
作者：
Li L;Eichten SR;Shimizu R;Petsch K;Yeh CT;Wu W;Chettoor AM;Givan SA;Cole RA;Fowler JE;Evans MM;Scanlon MJ;Yu J;Schnable PS;Timmermans MC;Springer NM;Muehlbauer GJ
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Muehlbauer GJ
影响因子：
6.3
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Kim SK;Park JH
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Park JH
三七根转录组分析揭示了假定的三萜皂苷生物合成基因和遗传标记
影响因子：
4.4
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Luo H;Sun C;Sun Y;Wu Q;Li Y;Song J;Niu Y;Cheng X;Xu H;Li C;Liu J;Steinmetz A;Chen S
通讯作者：
Chen S
影响因子：
14.9
作者：
Lagesen K;Hallin P;Rødland EA;Staerfeldt HH;Rognes T;Ussery DW
通讯作者：
Ussery DW
影响因子：
2.8
作者：
Lee, Jeongyeo;Han, Ching-Tack;Hur, Yoonkang
通讯作者：
Hur, Yoonkang