The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng
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)...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2015-01-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00696/full |
| _version_ | 1811199600578527232 |
|---|---|
| author | Yongbing eZhao Yongbing eZhao Jinlong eYin Haiyan eGuo Yuyu eZhang Yuyu eZhang Wen eXiao Wen eXiao Chen eSun Chen eSun Jiayan eWu Xiaobo eQu Jun eYu Xumin eWang Jingfa eXiao |
| author_facet | Yongbing eZhao Yongbing eZhao Jinlong eYin Haiyan eGuo Yuyu eZhang Yuyu eZhang Wen eXiao Wen eXiao Chen eSun Chen eSun Jiayan eWu Xiaobo eQu Jun eYu Xumin eWang Jingfa eXiao |
| author_sort | Yongbing eZhao |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T01:50:15Z |
| format | Article |
| id | doaj.art-40897713878a43e591df7acdedbb8b99 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T01:50:15Z |
| publishDate | 2015-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-40897713878a43e591df7acdedbb8b992022-12-22T03:52:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-01-01510.3389/fpls.2014.00696119215The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginsengYongbing eZhao0Yongbing eZhao1Jinlong eYin2Haiyan eGuo3Yuyu eZhang4Yuyu eZhang5Wen eXiao6Wen eXiao7Chen eSun8Chen eSun9Jiayan eWu10Xiaobo eQu11Jun eYu12Xumin eWang13Jingfa eXiao14Beijing institute of Genomics, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesChangchun University of Chinese MedicineBeijing institute of Genomics, Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesChangchun University of Chinese MedicineBeijing institute of Genomics, Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesBeijing institute of Genomics, Chinese Academy of SciencesPanax 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00696/fullSNPComparative genomicsPanax ginsengChloroplast genomeminor allele |
| spellingShingle | Yongbing eZhao Yongbing eZhao Jinlong eYin Haiyan eGuo Yuyu eZhang Yuyu eZhang Wen eXiao Wen eXiao Chen eSun Chen eSun Jiayan eWu Xiaobo eQu Jun eYu Xumin eWang Jingfa eXiao The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng Frontiers in Plant Science SNP Comparative genomics Panax ginseng Chloroplast genome minor allele |
| title | The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng |
| title_full | The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng |
| title_fullStr | The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng |
| title_full_unstemmed | The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng |
| title_short | The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng |
| title_sort | complete chloroplast genome provides insight into the evolution and polymorphism of panax ginseng |
| topic | SNP Comparative genomics Panax ginseng Chloroplast genome minor allele |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00696/full |
| work_keys_str_mv | AT yongbingezhao thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yongbingezhao thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jinlongeyin thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT haiyaneguo thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yuyuezhang thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yuyuezhang thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT wenexiao thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT wenexiao thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT chenesun thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT chenesun thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jiayanewu thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT xiaoboequ thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT juneyu thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT xuminewang thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jingfaexiao thecompletechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yongbingezhao completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yongbingezhao completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jinlongeyin completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT haiyaneguo completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yuyuezhang completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT yuyuezhang completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT wenexiao completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT wenexiao completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT chenesun completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT chenesun completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jiayanewu completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT xiaoboequ completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT juneyu completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT xuminewang completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng AT jingfaexiao completechloroplastgenomeprovidesinsightintotheevolutionandpolymorphismofpanaxginseng |