The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)
Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2018-12-01
|
| Series: | Plant Diversity |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265918301057 |
| _version_ | 1828910311951826944 |
|---|---|
| author | Changkun Liu Zhenyan Yang Lifang Yang Junbo Yang Yunheng Ji |
| author_facet | Changkun Liu Zhenyan Yang Lifang Yang Junbo Yang Yunheng Ji |
| author_sort | Changkun Liu |
| collection | DOAJ |
| description | Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species. Keywords: Araliaceae, Plastome, Comparative genomics, Panax stipuleanatus, Phylogenomics |
| first_indexed | 2024-12-13T18:41:42Z |
| format | Article |
| id | doaj.art-8e43e94179504fd289dfc9ee1b3b1738 |
| institution | Directory Open Access Journal |
| issn | 2468-2659 |
| language | English |
| last_indexed | 2024-12-13T18:41:42Z |
| publishDate | 2018-12-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj.art-8e43e94179504fd289dfc9ee1b3b17382022-12-21T23:35:13ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592018-12-01406265276The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)Changkun Liu0Zhenyan Yang1Lifang Yang2Junbo Yang3Yunheng Ji4Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; School of Life Science, Yunnan University, Kunming 650091, ChinaGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Corresponding author.Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Corresponding author.Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species. Keywords: Araliaceae, Plastome, Comparative genomics, Panax stipuleanatus, Phylogenomicshttp://www.sciencedirect.com/science/article/pii/S2468265918301057 |
| spellingShingle | Changkun Liu Zhenyan Yang Lifang Yang Junbo Yang Yunheng Ji The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) Plant Diversity |
| title | The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) |
| title_full | The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) |
| title_fullStr | The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) |
| title_full_unstemmed | The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) |
| title_short | The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae) |
| title_sort | complete plastome of panax stipuleanatus comparative and phylogenetic analyses of the genus panax araliaceae |
| url | http://www.sciencedirect.com/science/article/pii/S2468265918301057 |
| work_keys_str_mv | AT changkunliu thecompleteplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT zhenyanyang thecompleteplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT lifangyang thecompleteplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT junboyang thecompleteplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT yunhengji thecompleteplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT changkunliu completeplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT zhenyanyang completeplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT lifangyang completeplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT junboyang completeplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae AT yunhengji completeplastomeofpanaxstipuleanatuscomparativeandphylogeneticanalysesofthegenuspanaxaraliaceae |