Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera
<i>Curcuma</i> is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of <i>Curcuma</i> (Chinese <i>Curcuma</i>, a recent Qinghai–Tibetan Platea...
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MDPI AG
2022-02-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/13/2/280 |
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| author | Heng Liang Jiabin Deng Gang Gao Chunbang Ding Li Zhang Ruiwu Yang |
| author_facet | Heng Liang Jiabin Deng Gang Gao Chunbang Ding Li Zhang Ruiwu Yang |
| author_sort | Heng Liang |
| collection | DOAJ |
| description | <i>Curcuma</i> is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of <i>Curcuma</i> (Chinese <i>Curcuma</i>, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese <i>Curcuma</i> species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese <i>Curcuma</i> with varying degrees of support using different methods and datasets. |
| first_indexed | 2024-03-09T21:56:30Z |
| format | Article |
| id | doaj.art-3ad2f54169f74fdaa7f74c68f1295301 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-09T21:56:30Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-3ad2f54169f74fdaa7f74c68f12953012023-11-23T19:57:03ZengMDPI AGForests1999-49072022-02-0113228010.3390/f13020280Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification GeneraHeng Liang0Jiabin Deng1Gang Gao2Chunbang Ding3Li Zhang4Ruiwu Yang5College of Life Science, Sichuan Agricultural University, Yaan 625014, ChinaSchool of Geography and Resources, Guizhou Education University, Guiyang 550018, ChinaFaculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, ChinaCollege of Life Science, Sichuan Agricultural University, Yaan 625014, ChinaCollege of Science, Sichuan Agricultural University, Yaan 625014, ChinaCollege of Life Science, Sichuan Agricultural University, Yaan 625014, China<i>Curcuma</i> is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of <i>Curcuma</i> (Chinese <i>Curcuma</i>, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese <i>Curcuma</i> species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese <i>Curcuma</i> with varying degrees of support using different methods and datasets.https://www.mdpi.com/1999-4907/13/2/280ddRADplastid genomes<i>Curcuma</i>rapid radiationphylogeny |
| spellingShingle | Heng Liang Jiabin Deng Gang Gao Chunbang Ding Li Zhang Ruiwu Yang Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera Forests ddRAD plastid genomes <i>Curcuma</i> rapid radiation phylogeny |
| title | Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera |
| title_full | Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera |
| title_fullStr | Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera |
| title_full_unstemmed | Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera |
| title_short | Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese <i>Curcuma</i> (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera |
| title_sort | incompatibility phylogenetic signals between double digest restriction site associated dna sequencing and plastid genomes in chinese i curcuma i zingiberaceae a recent qinghai tibetan plateau diversification genera |
| topic | ddRAD plastid genomes <i>Curcuma</i> rapid radiation phylogeny |
| url | https://www.mdpi.com/1999-4907/13/2/280 |
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