title: Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes.
abstract: The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. caohongzhe1986@hotmail.com.
authors: Hongzhe
authors: H
authors: Cao
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. nzaman_global@yahoo.com.
authors: Mohammed
authors: M
authors: Nuruzzaman
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. haoxiu1990@163.com.
authors: Hao
authors: H
authors: Xiu
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. huangjj1985@126.com.
authors: Jingjia
authors: J
authors: Huang
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. wukunlu@163.com.
authors: Kunlu
authors: K
authors: Wu
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. chenxianghui@163.com.
authors: Xianghui
authors: X
authors: Chen
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. lijijia1986@126.com.
authors: Jijia
authors: J
authors: Li
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. wangli@mail.csu.edu.cn.
authors: Li
authors: L
authors: Wang
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. jhjeong@126.com.
authors: Ji-Hak
authors: JH
authors: Jeong
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. sunjpark@126.com.
authors: Sun-Jin
authors: SJ
authors: Park
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. Yangfang2010@csu.edu.cn.
authors: Fang
authors: F
authors: Yang
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. lijijia1986@126.com.
authors: Junli
authors: J
authors: Luo
authors: Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China. luozhiyong@csu.edu.cn.
authors: Zhiyong
authors: Z
authors: Luo
mesh_terms: D000085:Acetates / Q000494:pharmacology*; D003517:Cyclopentanes / Q000494:pharmacology*; D030541:Databases, Genetic; D030562:Databases, Protein; D015536:Down-Regulation / Q000187:drug effects; D000431:Ethanol / Q000494:pharmacology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D058685:Genetic Pleiotropy / Q000187:drug effects; D036145:Ginsenosides / Q000096:biosynthesis*; D058977:Molecular Sequence Annotation; D054883:Oxylipins / Q000494:pharmacology*; D005894:Panax / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D017422:Sequence Analysis, DNA; D015854:Up-Regulation / Q000187:drug effects
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D036145:Ginsenosides; D054883:Oxylipins; D010940:Plant Proteins; D000431:Ethanol; C072239:methyl jasmonate
references: Mol Biol Rep. 2010 Oct;37(7):3465-72
references: 19943115
references: Annu Rev Plant Biol. 2009;60:305-33
references: 19575585
references: Yao Xue Xue Bao. 2010 Jul;45(7):807-12
references: 20931775
references: Trends Plant Sci. 2005 Nov;10(11):542-9
references: 16214386
references: Molecules. 2014;19(5):5777-89
references: 24802988
references: Chin J Integr Med. 2009 Dec;15(6):403-8
references: 20082243
references: J Korean Med Sci. 2001 Dec;16 Suppl:S3-5
references: 11748372
references: Annu Rev Pharmacol Toxicol. 2005;45:1-25
references: 15832443
references: Plant Cell Rep. 2005 Jan;23(8):557-66
references: 15538577
references: Cell Res. 2014 Jun;24(6):770-3
references: 24603359
references: FEBS Lett. 2006 Feb 13;580(4):1123-30
references: 16506311
references: Mol Plant Pathol. 2009 Sep;10(5):651-63
references: 19694955
references: FEBS Lett. 2006 Feb 13;580(4):1183-91
references: 16364309
references: Plant Cell Rep. 2014 Mar;33(3):393-400
references: 24258243
references: Phytochemistry. 2010 Jan;71(1):36-46
references: 19857882
references: Plant J. 2012 Dec;72(5):745-57
references: 22804955
references: FEBS Lett. 2002 May 8;518(1-3):164-8
references: 11997039
references: Genetika. 2010 Jul;46(7):932-9
references: 20795497
references: Nature. 2012 Mar 15;483(7389):341-4
references: 22398443
references: Annu Rev Genomics Hum Genet. 2009;10:135-51
references: 19715439
references: Nat Biotechnol. 2010 May;28(5):421-3
references: 20458303
references: BMC Genomics. 2010;11:726
references: 21182800
references: Plant Cell Physiol. 2006 Dec;47(12):1653-62
references: 17088293
references: Int J Mol Sci. 2012;13(5):5729-39
references: 22754327
references: Biochem Biophys Res Commun. 2013 Feb 1;431(1):111-5
references: 23266612
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references: 16845012
references: Mol Ecol. 2013 Feb;22(3):620-34
references: 22998089
references: BMC Genomics. 2013;14:245
references: 23577925
references: J Integr Plant Biol. 2011 Oct;53(10):800-13
references: 21910825
references: Acta Pharmacol Sin. 2008 Sep;29(9):1103-8
references: 18718179
references: PLoS One. 2014;9(3):e91740
references: 24626227
references: Mol Biol Rep. 2013 Nov;40(11):6195-204
references: 24065536
references: Nat Biotechnol. 2011 Jul;29(7):644-52
references: 21572440
references: Plant Cell Rep. 2003 Oct;22(3):224-30
references: 12920566
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Appl Microbiol Biotechnol. 2001 Nov;57(4):482-8
references: 11762592
references: Phytochemistry. 2004 Feb;65(3):261-91
references: 14751299
references: Brief Funct Genomics. 2010 Mar;9(2):118-28
references: 20130067
references: Int J Mol Sci. 2013 Jan 31;14(2):2980-95
references: 23434653
references: Nat Methods. 2008 Jan;5(1):16-8
references: 18165802
references: Nat Prod Commun. 2010 Jul;5(7):1147-58
references: 20734961
references: Biotechnol Lett. 2004 Nov;26(21):1619-22
references: 15604808
references: J Ginseng Res. 2014 Oct 15;38(4):278-88
references: 25379008
references: Appl Microbiol Biotechnol. 2005 Apr;67(2):197-201
references: 15578180
references: Plant Cell Physiol. 2004 Aug;45(8):976-84
references: 15356323
references: Mol Immunol. 2009 Sep;46(15):2918-30
references: 19631987
references: Plant Physiol Biochem. 2013 Oct;71:203-11
references: 23968928
references: BMC Genomics. 2010;11:262
references: 20416102
references: J Integr Plant Biol. 2014 Aug;56(8):729-40
references: 24645852
references: Plant Cell Rep. 2011 Sep;30(9):1593-601
references: 21484331
references: Ann Bot. 2007 Oct;100(4):681-97
references: 17513307
references: Plant Biotechnol J. 2009 May;7(4):334-46
references: 19207216
references: Nature. 2007 Aug 9;448(7154):659-60
references: 17687317
references: BMC Genomics. 2013;14:564
references: 23957709
references: Science. 2000 Jul 14;289(5477):295-7
references: 10894776
references: Annu Rev Biochem. 2008;77:521-55
references: 18518825
references: Physiol Plant. 2010 Feb;138(2):134-49
references: 19947964
references: Plant Biol (Stuttg). 2008 Jul;10(4):415-21
references: 18557901
references: BMC Genomics. 2011 Dec 23;12 Suppl 5:S5
references: 22369100
references: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references: 10786296
references: Mol Phylogenet Evol. 1996 Oct;6(2):167-77
references: 8899721
references: Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2389-93
references: 11607285
references: Plant Cell Rep. 2006 Jun;25(6):599-606
references: 16397780