Comprehensive analysis of Panax ginseng root transcriptomes

BMC Plant Biology

Research Article

Murukarthick Jayakodi¹  Ho Jun Joh¹  Hyun Oh Lee¹  Sang-Choon Lee¹  Nam-Hoon Kim¹  Yun Sun Lee¹  Woojong Jang¹  Hyun-Seung Park¹  Tae-Jin Yang² 

[1] Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, 232-916, Pyeongchang, Republic of Korea;

关键词: Panax ginseng;    Root;    Transcriptomics;    Ginsenoside;    RNA-seq;   

DOI  :  10.1186/s12870-015-0527-0

 received in 2015-03-16, accepted in 2015-05-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundKorean 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.ResultsHere, 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.ConclusionOur analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.

【 授权许可】

Unknown   
© Jayakodi et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.