Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends
Abstract Background Polygonatum cyrtonema Hua, a valuable medicinal and edible plant in China, has been increasingly cultivated to produce nutritional and health products to meet market demand. However, the absence of the mitochondrial genome hinders the research of evolutionary analysis, artificial...
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| Format: | Article |
| Language: | English |
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BMC
2025-08-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-07074-9 |
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| author | Haoxiang Luo Fengxiao Ren Guochao Cao Dekai Wang Qiaojun Jia |
| author_facet | Haoxiang Luo Fengxiao Ren Guochao Cao Dekai Wang Qiaojun Jia |
| author_sort | Haoxiang Luo |
| collection | DOAJ |
| description | Abstract Background Polygonatum cyrtonema Hua, a valuable medicinal and edible plant in China, has been increasingly cultivated to produce nutritional and health products to meet market demand. However, the absence of the mitochondrial genome hinders the research of evolutionary analysis, artificial cultivation, and medicinal resource development. This study aimed to systematically characterize the mitochondrial genome of P. cyrtonema and perform a preliminary bioinformatic analysis. Result In this study, the mitochondrial genome of P. cyrtonema was assembled and annotated by combining Illumina reads with long-read Oxford Nanopore Technologies, which formed a complex non-circular structure covering 664,991 bp in length, with 33 protein-coding genes, 20 tRNAs, and 3 rRNAs. Overall, a total of 194 simple repeats, 24 tandem repeats, and 294 dispersed repeats were identified, and 599 RNA editing sites were predicted, all of which were C-to-T types. In particular, 29 homologous fragments between the chloroplast and mitochondrial genome were detected and accounted for 2.4% of the mitochondrial genome. In addition, codon usage analysis, nucleotide diversity analysis, and Ka/Ks analysis suggested a slower rate of evolution and a relatively conserved structure of the mitochondrial genome. Phylogenetic relationships based on 33 species demonstrated that P. cyrtonema was most closely related to Polygonatum sibiricum. Conclusion Our results provide comprehensive information on the mitochondrial genome of P. cyrtonema, and demonstrate the availability of mitochondrial genome-based taxonomic classification for Polygonatum Mill.. Moreover, it offers a valuable foundation for future research in the cultivation and pharmacological development within Polygonatum species. |
| format | Article |
| id | doaj-art-ffd368b9000840f5be4542389d98faaf |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-ffd368b9000840f5be4542389d98faaf2025-08-24T11:16:41ZengBMCBMC Plant Biology1471-22292025-08-0125111710.1186/s12870-025-07074-9Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trendsHaoxiang Luo0Fengxiao Ren1Guochao Cao2Dekai Wang3Qiaojun Jia4College of Life Sciences and Medicine, Zhejiang Sci-Tech UniversityCollege of Life Sciences and Medicine, Zhejiang Sci-Tech UniversityCollege of Life Sciences and Medicine, Zhejiang Sci-Tech UniversityCollege of Life Sciences and Medicine, Zhejiang Sci-Tech UniversityCollege of Life Sciences and Medicine, Zhejiang Sci-Tech UniversityAbstract Background Polygonatum cyrtonema Hua, a valuable medicinal and edible plant in China, has been increasingly cultivated to produce nutritional and health products to meet market demand. However, the absence of the mitochondrial genome hinders the research of evolutionary analysis, artificial cultivation, and medicinal resource development. This study aimed to systematically characterize the mitochondrial genome of P. cyrtonema and perform a preliminary bioinformatic analysis. Result In this study, the mitochondrial genome of P. cyrtonema was assembled and annotated by combining Illumina reads with long-read Oxford Nanopore Technologies, which formed a complex non-circular structure covering 664,991 bp in length, with 33 protein-coding genes, 20 tRNAs, and 3 rRNAs. Overall, a total of 194 simple repeats, 24 tandem repeats, and 294 dispersed repeats were identified, and 599 RNA editing sites were predicted, all of which were C-to-T types. In particular, 29 homologous fragments between the chloroplast and mitochondrial genome were detected and accounted for 2.4% of the mitochondrial genome. In addition, codon usage analysis, nucleotide diversity analysis, and Ka/Ks analysis suggested a slower rate of evolution and a relatively conserved structure of the mitochondrial genome. Phylogenetic relationships based on 33 species demonstrated that P. cyrtonema was most closely related to Polygonatum sibiricum. Conclusion Our results provide comprehensive information on the mitochondrial genome of P. cyrtonema, and demonstrate the availability of mitochondrial genome-based taxonomic classification for Polygonatum Mill.. Moreover, it offers a valuable foundation for future research in the cultivation and pharmacological development within Polygonatum species.https://doi.org/10.1186/s12870-025-07074-9Mitochondrial genomePhylogenetic evolutionPolygonatum cyrtonema HuaRepeated sequencesRNA editing |
| spellingShingle | Haoxiang Luo Fengxiao Ren Guochao Cao Dekai Wang Qiaojun Jia Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends BMC Plant Biology Mitochondrial genome Phylogenetic evolution Polygonatum cyrtonema Hua Repeated sequences RNA editing |
| title | Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends |
| title_full | Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends |
| title_fullStr | Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends |
| title_full_unstemmed | Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends |
| title_short | Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends |
| title_sort | complete mitochondrial genome of polygonatum cyrtonema hua reveals variation diversity and evolutionary trends |
| topic | Mitochondrial genome Phylogenetic evolution Polygonatum cyrtonema Hua Repeated sequences RNA editing |
| url | https://doi.org/10.1186/s12870-025-07074-9 |
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