Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus
Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1050040/full |
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| author | Dan Liu Dan Liu Kai Qu Yangchen Yuan Yangchen Yuan Zhiheng Zhao Ying Chen Biao Han Wei Li Yousry A. El-Kassaby Yangyang Yin Xiaoman Xie Boqiang Tong Hongshan Liu |
| author_facet | Dan Liu Dan Liu Kai Qu Yangchen Yuan Yangchen Yuan Zhiheng Zhao Ying Chen Biao Han Wei Li Yousry A. El-Kassaby Yangyang Yin Xiaoman Xie Boqiang Tong Hongshan Liu |
| author_sort | Dan Liu |
| collection | DOAJ |
| description | Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants. |
| first_indexed | 2024-04-10T20:20:44Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T20:20:44Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-27418a553d284eabbab4e7fa55a852af2023-01-25T18:14:20ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10500401050040Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genusDan Liu0Dan Liu1Kai Qu2Yangchen Yuan3Yangchen Yuan4Zhiheng Zhao5Ying Chen6Biao Han7Wei Li8Yousry A. El-Kassaby9Yangyang Yin10Xiaoman Xie11Boqiang Tong12Hongshan Liu13Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, ChinaHebei Hongya Mountain State-Owned Forest Farm, Baoding, ChinaGuangxi Forestry Research Institute, Guangxi Key Laboratory of Special Non-wood Forest Cultivation &; Utilization, Nanning, ChinaForestry Protection and Development Service Center of Shandong Province, Jinan, ChinaShandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaDepartment of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, CanadaWuhan Benagen Technology Co., Ltd, Wuhan, ChinaShandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, ChinaShandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, ChinaHebei Hongya Mountain State-Owned Forest Farm, Baoding, ChinaClematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.https://www.frontiersin.org/articles/10.3389/fgene.2022.1050040/fullclematismitochondrial genomeorganelle genomeClematis acerifoliaphylogenetic relationshiprepeats |
| spellingShingle | Dan Liu Dan Liu Kai Qu Yangchen Yuan Yangchen Yuan Zhiheng Zhao Ying Chen Biao Han Wei Li Yousry A. El-Kassaby Yangyang Yin Xiaoman Xie Boqiang Tong Hongshan Liu Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus Frontiers in Genetics clematis mitochondrial genome organelle genome Clematis acerifolia phylogenetic relationship repeats |
| title | Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| title_full | Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| title_fullStr | Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| title_full_unstemmed | Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| title_short | Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| title_sort | complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered clematis acerifolia the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus |
| topic | clematis mitochondrial genome organelle genome Clematis acerifolia phylogenetic relationship repeats |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1050040/full |
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