title: The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng.
abstract: Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing.
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China.
authors: Yongbing
authors: Y
authors: Zhao
authors: School of Pharmaceutical Sciences, Changchun University of Chinese Medicine Changchun, China.
authors: Jinlong
authors: J
authors: Yin
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors: Haiyan
authors: H
authors: Guo
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China.
authors: Yuyu
authors: Y
authors: Zhang
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China.
authors: Wen
authors: W
authors: Xiao
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China.
authors: Chen
authors: C
authors: Sun
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors: Jiayan
authors: J
authors: Wu
authors: School of Pharmaceutical Sciences, Changchun University of Chinese Medicine Changchun, China.
authors: Xiaobo
authors: X
authors: Qu
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors: Jun
authors: J
authors: Yu
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors: Xumin
authors: X
authors: Wang
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors: Jingfa
authors: J
authors: Xiao
keywords: Panax ginseng; SNP; chloroplast genome; comparative genomics; minor allele
references: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9
references: 20439314
references: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19363-8
references: 18048334
references: PLoS One. 2010 Sep 15;5(9):e12762
references: 20856810
references: Mol Phylogenet Evol. 2004 Jun;31(3):894-903
references: 15120387
references: Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18301-6
references: 22042846
references: PLoS Genet. 2013;9(1):e1003211
references: 23349635
references: BMC Evol Biol. 2008 Oct 07;8:275
references: 18840274
references: Bioinformatics. 2004 Nov 22;20(17):3252-5
references: 15180927
references: Mol Biol Evol. 2007 Jun;24(6):1366-79
references: 17383970
references: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19369-74
references: 18048330
references: Int J Mol Sci. 2012 Oct 03;13(10):12608-28
references: 23202917
references: Plant J. 2000 Apr;22(2):97-104
references: 10792825
references: PLoS One. 2013;8(3):e59620
references: 23527231
references: Genome Res. 2008 May;18(5):821-9
references: 18349386
references: Chin J Integr Med. 2012 Jul;18(7):548-55
references: 22772919
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: DNA Res. 2011 Apr;18(2):93-105
references: 21444340
references: Mol Gen Genet. 1996 Aug 27;252(1-2):195-206
references: 8804393
references: Comp Funct Genomics. 2012;2012:628204
references: 23326209
references: PLoS One. 2013 Nov 26;8(11):e80508
references: 24303020
references: Annu Rev Genet. 2001;35:125-48
references: 11700280
references: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references: 9023104
references: Genome Biol Evol. 2010;2:504-17
references: 20651328
references: Plant Methods. 2011 Nov 29;7:38
references: 22126655
references: Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4623-8
references: 20176954
references: BMC Plant Biol. 2012 May 01;12:61
references: 22548759
references: PLoS One. 2012;7(12):e52974
references: 23285238
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: PLoS One. 2013;8(1):e53537
references: 23308248
references: Am J Bot. 2013 May;100(5):930-8
references: 23594914
references: Bioinformatics. 2010 Mar 1;26(5):589-95
references: 20080505
references: Genome. 2007 Feb;50(2):180-7
references: 17546083
references: Methods Enzymol. 2005;395:348-84
references: 15865976
references: Int Rev Cytol. 1996;165:207-34
references: 8900960
references: Annu Rev Plant Physiol Plant Mol Biol. 2000 Jun;51:111-140
references: 15012188
references: PLoS Genet. 2009 Jun;5(6):e1000504
references: 19503597
references: Plant Cell. 1999 Apr;11(4):549-56
references: 10213777
references: DNA Res. 2004 Aug 31;11(4):247-61
references: 15500250
references: EMBO J. 1986 Sep;5(9):2043-2049
references: 16453699
references: PLoS One. 2012;7(7):e42041
references: 22870184
references: PLoS One. 2012;7(1):e30531
references: 22291979
references: Annu Rev Genet. 1985;19:325-54
references: 3936406
references: BMC Ecol. 2013 Mar 14;13:8
references: 23497206
references: Mol Cells. 2012 May;33(5):497-508
references: 22555800
references: PLoS One. 2012;7(5):e35872
references: 22606240
references: J Ethnopharmacol. 2013 May 20;147(2):509-16
references: 23545455
references: Bioinformatics. 2009 Jun 1;25(11):1451-2
references: 19346325
references: Plant Mol Biol. 2011 Jul;76(3-5):273-97
references: 21424877
references: Plant Physiol. 2004 May;135(1):412-20
references: 15122023
references: BMC Genomics. 2012 Nov 23;13:661
references: 23173617
references: PLoS One. 2013;8(2):e57607
references: 23460883
references: PLoS One. 2013;8(2):e57533
references: 23460871
references: PLoS One. 2013 Oct 18;8(10):e77965
references: 24205047
references: Am J Bot. 2011 May;98(5):e123-6
references: 21613178
references: BMC Evol Biol. 2013 Apr 18;13:84
references: 23597078
references: Curr Genet. 2007 Nov;52(5-6):267-74
references: 17957369
references: BMC Evol Biol. 2008 Jan 31;8:36
references: 18237435
references: BMC Biol. 2009 Dec 02;7:84
references: 19954512
references: PLoS One. 2006 Dec 20;1:e8
references: 17183712
references: Phytother Res. 2012 Oct;26(10):1579-80
references: 22318923
references: Am J Bot. 2012 Jun;99(6):e240-4
references: 22615305
references: Plant Mol Biol. 2001 Feb;45(3):307-15
references: 11292076
references: Bioinformatics. 2010 Aug 1;26(15):1899-900
references: 20427515
references: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
references: 17531802