Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis
Root rot has been a major problem for cultivated populations of Coptis chinensis var. chinensis in recent years. C. chinensis var. brevisepala, the closest wild relative of C. chinensis var. chinensis, has a scattered distribution across southwestern China and is an important wild resource. Genetic...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.923600/full |
| _version_ | 1818466229598289920 |
|---|---|
| author | Yiheng Wang Jiahui Sun Zhenyu Zhao Chao Xu Ping Qiao Ping Qiao Sheng Wang Mengli Wang Zegang Xu Qingjun Yuan Lanping Guo Luqi Huang |
| author_facet | Yiheng Wang Jiahui Sun Zhenyu Zhao Chao Xu Ping Qiao Ping Qiao Sheng Wang Mengli Wang Zegang Xu Qingjun Yuan Lanping Guo Luqi Huang |
| author_sort | Yiheng Wang |
| collection | DOAJ |
| description | Root rot has been a major problem for cultivated populations of Coptis chinensis var. chinensis in recent years. C. chinensis var. brevisepala, the closest wild relative of C. chinensis var. chinensis, has a scattered distribution across southwestern China and is an important wild resource. Genetic diversity is associated with greater evolutionary potential and resilience of species or populations and is important for the breeding and conservation of species. Here, we conducted multiplexed massively parallel sequencing of the plastomes of 227 accessions of wild and cultivated C. chinensis using 111 marker pairs to study patterns of genetic diversity, population structure, and phylogeography among wild and cultivated C. chinensis populations. Wild and cultivated resources diverged approximately 2.83 Mya. The cultivated resources experienced a severe genetic bottleneck and possess highly mixed germplasm. However, high genetic diversity has been retained in the wild resources, and subpopulations in different locations differed in genotype composition. The significant divergence in the genetic diversity of wild and cultivated resources indicates that they require different conservation strategies. Wild resources require in situ conservation strategies aiming to expand population sizes while maintaining levels of genetic diversity; by contrast, germplasm resource nurseries with genotypes of cultivated resources and planned distribution measures are needed for the conservation of cultivated resources to prevent cultivated populations from undergoing severe genetic bottlenecks. The results of this study provide comprehensive insights into the genetic diversity, population structure, and phylogeography of C. chinensis and will facilitate future breeding and conservation efforts. |
| first_indexed | 2024-04-13T20:55:19Z |
| format | Article |
| id | doaj.art-611039a3984449759093a93903d33c1d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T20:55:19Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-611039a3984449759093a93903d33c1d2022-12-22T02:30:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-07-011310.3389/fpls.2022.923600923600Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensisYiheng Wang0Jiahui Sun1Zhenyu Zhao2Chao Xu3Ping Qiao4Ping Qiao5Sheng Wang6Mengli Wang7Zegang Xu8Qingjun Yuan9Lanping Guo10Luqi Huang11National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaAcademician Workstation, Jiangxi University of Traditional Chinese Medicine, Nanchang, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaLichuan Jianzhuxi Huanglian Cooperative, Lichuan, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaRoot rot has been a major problem for cultivated populations of Coptis chinensis var. chinensis in recent years. C. chinensis var. brevisepala, the closest wild relative of C. chinensis var. chinensis, has a scattered distribution across southwestern China and is an important wild resource. Genetic diversity is associated with greater evolutionary potential and resilience of species or populations and is important for the breeding and conservation of species. Here, we conducted multiplexed massively parallel sequencing of the plastomes of 227 accessions of wild and cultivated C. chinensis using 111 marker pairs to study patterns of genetic diversity, population structure, and phylogeography among wild and cultivated C. chinensis populations. Wild and cultivated resources diverged approximately 2.83 Mya. The cultivated resources experienced a severe genetic bottleneck and possess highly mixed germplasm. However, high genetic diversity has been retained in the wild resources, and subpopulations in different locations differed in genotype composition. The significant divergence in the genetic diversity of wild and cultivated resources indicates that they require different conservation strategies. Wild resources require in situ conservation strategies aiming to expand population sizes while maintaining levels of genetic diversity; by contrast, germplasm resource nurseries with genotypes of cultivated resources and planned distribution measures are needed for the conservation of cultivated resources to prevent cultivated populations from undergoing severe genetic bottlenecks. The results of this study provide comprehensive insights into the genetic diversity, population structure, and phylogeography of C. chinensis and will facilitate future breeding and conservation efforts.https://www.frontiersin.org/articles/10.3389/fpls.2022.923600/fullCoptis chinensiswild and cultivatedgenetic diversityphylogeographypopulation structuremassively parallel sequencing |
| spellingShingle | Yiheng Wang Jiahui Sun Zhenyu Zhao Chao Xu Ping Qiao Ping Qiao Sheng Wang Mengli Wang Zegang Xu Qingjun Yuan Lanping Guo Luqi Huang Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis Frontiers in Plant Science Coptis chinensis wild and cultivated genetic diversity phylogeography population structure massively parallel sequencing |
| title | Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis |
| title_full | Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis |
| title_fullStr | Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis |
| title_full_unstemmed | Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis |
| title_short | Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis |
| title_sort | multiplexed massively parallel sequencing of plastomes provides insights into the genetic diversity population structure and phylogeography of wild and cultivated coptis chinensis |
| topic | Coptis chinensis wild and cultivated genetic diversity phylogeography population structure massively parallel sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.923600/full |
| work_keys_str_mv | AT yihengwang multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT jiahuisun multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT zhenyuzhao multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT chaoxu multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT pingqiao multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT pingqiao multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT shengwang multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT mengliwang multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT zegangxu multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT qingjunyuan multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT lanpingguo multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis AT luqihuang multiplexedmassivelyparallelsequencingofplastomesprovidesinsightsintothegeneticdiversitypopulationstructureandphylogeographyofwildandcultivatedcoptischinensis |