Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae
Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within Polygonatum have long been controversia...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-06-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.882189/full |
| _version_ | 1811236129061470208 |
|---|---|
| author | Jing Wang Jing Wang Jun Qian Yuan Jiang Xiaochen Chen Baojiang Zheng Shilin Chen Fajian Yang Zhichao Xu Zhichao Xu Baozhong Duan |
| author_facet | Jing Wang Jing Wang Jun Qian Yuan Jiang Xiaochen Chen Baojiang Zheng Shilin Chen Fajian Yang Zhichao Xu Zhichao Xu Baozhong Duan |
| author_sort | Jing Wang |
| collection | DOAJ |
| description | Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within Polygonatum have long been controversial because of the complexity of their morphological variations and lack of high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering phylogenetic relationships in related families. In the present study, the complete cp genome of 26 species of Trib. Polygonateae were de novo assembled and characterized; all species exhibited a conserved quadripartite structure, that is, two inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, large single sequence (LSC) and small single sequence (SSC). A total of 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, and trnC-GCA-petN) that might be useful as potential molecular markers for identifying Polygonatum species were identified. The molecular clock analysis results showed that the divergence time of Polygonatum might occur at ∼14.71 Ma, and the verticillate leaf might be the ancestral state of this genus. Moreover, phylogenetic analysis based on 88 cp genomes strongly supported the monophyly of Polygonatum. The phylogenetic analysis also suggested that Heteropolygonatum may be the sister group of the Polygonatum, but the Disporopsis, Maianthemum, and Disporum may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of Polygonatum. |
| first_indexed | 2024-04-12T12:03:37Z |
| format | Article |
| id | doaj.art-91dc924786774ac7805ce99b22dbf517 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T12:03:37Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-91dc924786774ac7805ce99b22dbf5172022-12-22T03:33:47ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-06-011310.3389/fpls.2022.882189882189Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe PolygonateaeJing Wang0Jing Wang1Jun Qian2Yuan Jiang3Xiaochen Chen4Baojiang Zheng5Shilin Chen6Fajian Yang7Zhichao Xu8Zhichao Xu9Baozhong Duan10College of Pharmaceutical Science, Dali University, Dali, ChinaHeilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, ChinaCollege of Pharmaceutical Science, Dali University, Dali, ChinaCollege of Pharmaceutical Science, Dali University, Dali, ChinaHeilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, ChinaHeilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaBaoshan College of Traditional Chinese Medicine, Baoshan, ChinaCollege of Pharmaceutical Science, Dali University, Dali, ChinaHeilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, College of Life Science, Northeast Forestry University, Harbin, ChinaCollege of Pharmaceutical Science, Dali University, Dali, ChinaMembers of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within Polygonatum have long been controversial because of the complexity of their morphological variations and lack of high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering phylogenetic relationships in related families. In the present study, the complete cp genome of 26 species of Trib. Polygonateae were de novo assembled and characterized; all species exhibited a conserved quadripartite structure, that is, two inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, large single sequence (LSC) and small single sequence (SSC). A total of 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, and trnC-GCA-petN) that might be useful as potential molecular markers for identifying Polygonatum species were identified. The molecular clock analysis results showed that the divergence time of Polygonatum might occur at ∼14.71 Ma, and the verticillate leaf might be the ancestral state of this genus. Moreover, phylogenetic analysis based on 88 cp genomes strongly supported the monophyly of Polygonatum. The phylogenetic analysis also suggested that Heteropolygonatum may be the sister group of the Polygonatum, but the Disporopsis, Maianthemum, and Disporum may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of Polygonatum.https://www.frontiersin.org/articles/10.3389/fpls.2022.882189/fullPolygonatumchloroplast genomephylogeneticsdivergence timeTrib. Polygonateae |
| spellingShingle | Jing Wang Jing Wang Jun Qian Yuan Jiang Xiaochen Chen Baojiang Zheng Shilin Chen Fajian Yang Zhichao Xu Zhichao Xu Baozhong Duan Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae Frontiers in Plant Science Polygonatum chloroplast genome phylogenetics divergence time Trib. Polygonateae |
| title | Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae |
| title_full | Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae |
| title_fullStr | Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae |
| title_full_unstemmed | Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae |
| title_short | Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae |
| title_sort | comparative analysis of chloroplast genome and new insights into phylogenetic relationships of polygonatum and tribe polygonateae |
| topic | Polygonatum chloroplast genome phylogenetics divergence time Trib. Polygonateae |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.882189/full |
| work_keys_str_mv | AT jingwang comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT jingwang comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT junqian comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT yuanjiang comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT xiaochenchen comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT baojiangzheng comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT shilinchen comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT fajianyang comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT zhichaoxu comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT zhichaoxu comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae AT baozhongduan comparativeanalysisofchloroplastgenomeandnewinsightsintophylogeneticrelationshipsofpolygonatumandtribepolygonateae |