Phylogenomics and barcoding of Panax: toward the identification of ginseng species
Abstract Background The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecul...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-04-01
|
| Series: | BMC Evolutionary Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12862-018-1160-y |
| _version_ | 1819124058678099968 |
|---|---|
| author | V. Manzanilla A. Kool L. Nguyen Nhat H. Nong Van H. Le Thi Thu H. J. de Boer |
| author_facet | V. Manzanilla A. Kool L. Nguyen Nhat H. Nong Van H. Le Thi Thu H. J. de Boer |
| author_sort | V. Manzanilla |
| collection | DOAJ |
| description | Abstract Background The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. Results We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. Conclusions MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients. |
| first_indexed | 2024-12-22T07:18:13Z |
| format | Article |
| id | doaj.art-a71492f4d183459f9b99679e5948bcd0 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-22T07:18:13Z |
| publishDate | 2018-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-a71492f4d183459f9b99679e5948bcd02022-12-21T18:34:21ZengBMCBMC Evolutionary Biology1471-21482018-04-0118111410.1186/s12862-018-1160-yPhylogenomics and barcoding of Panax: toward the identification of ginseng speciesV. Manzanilla0A. Kool1L. Nguyen Nhat2H. Nong Van3H. Le Thi Thu4H. J. de Boer5The Natural History Museum, University of OsloThe Natural History Museum, University of OsloInstitute of Genome Research, Vietnam Academy of Science and TechnologyInstitute of Genome Research, Vietnam Academy of Science and TechnologyInstitute of Genome Research, Vietnam Academy of Science and TechnologyThe Natural History Museum, University of OsloAbstract Background The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. Results We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. Conclusions MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.http://link.springer.com/article/10.1186/s12862-018-1160-yBarcodingGenomeGinsengMarkermPTPNGS |
| spellingShingle | V. Manzanilla A. Kool L. Nguyen Nhat H. Nong Van H. Le Thi Thu H. J. de Boer Phylogenomics and barcoding of Panax: toward the identification of ginseng species BMC Evolutionary Biology Barcoding Genome Ginseng Marker mPTP NGS |
| title | Phylogenomics and barcoding of Panax: toward the identification of ginseng species |
| title_full | Phylogenomics and barcoding of Panax: toward the identification of ginseng species |
| title_fullStr | Phylogenomics and barcoding of Panax: toward the identification of ginseng species |
| title_full_unstemmed | Phylogenomics and barcoding of Panax: toward the identification of ginseng species |
| title_short | Phylogenomics and barcoding of Panax: toward the identification of ginseng species |
| title_sort | phylogenomics and barcoding of panax toward the identification of ginseng species |
| topic | Barcoding Genome Ginseng Marker mPTP NGS |
| url | http://link.springer.com/article/10.1186/s12862-018-1160-y |
| work_keys_str_mv | AT vmanzanilla phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies AT akool phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies AT lnguyennhat phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies AT hnongvan phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies AT hlethithu phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies AT hjdeboer phylogenomicsandbarcodingofpanaxtowardtheidentificationofginsengspecies |