Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships
Aconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the...
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.878182/full |
| _version_ | 1818007448622989312 |
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| author | Conglong Xia Conglong Xia Manjiong Wang Yunhui Guan Jian Li Jian Li |
| author_facet | Conglong Xia Conglong Xia Manjiong Wang Yunhui Guan Jian Li Jian Li |
| author_sort | Conglong Xia |
| collection | DOAJ |
| description | Aconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of Aconitum species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of Aconitum species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 (A. stylosum) to 155,921 bp (A. vilmoinianum), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 (A. vilmoinianum) to 132 (A. ramulosum), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 Aconitum chloroplast genomes, including ten Aconitum chloroplast genomes and other sequenced Aconitum species. A total of 48–79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including trnK-UUU-trnQ-UGG, psbD, ndhJ-ndhK, clpP, psbH-petB, ycf1, and trnA-UGC-trnI-GAU, respectively. The phylogenetic trees of ten Aconitum species and other Aconitum species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among Aconitum species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of Aconitum species and an important reference and basis for Ranunculaceae species identification and phylogeny. |
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| spelling | doaj.art-bd5218bfbb39435c8b7a942d1b36013d2022-12-22T02:10:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-05-011310.3389/fgene.2022.878182878182Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic RelationshipsConglong Xia0Conglong Xia1Manjiong Wang2Yunhui Guan3Jian Li4Jian Li5State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, ChinaCollege of Pharmacy, Dali University, Dali, ChinaState Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, ChinaCollege of Pharmacy, Dali University, Dali, ChinaState Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, ChinaCollege of Pharmacy, Dali University, Dali, ChinaAconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of Aconitum species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of Aconitum species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 (A. stylosum) to 155,921 bp (A. vilmoinianum), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 (A. vilmoinianum) to 132 (A. ramulosum), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 Aconitum chloroplast genomes, including ten Aconitum chloroplast genomes and other sequenced Aconitum species. A total of 48–79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including trnK-UUU-trnQ-UGG, psbD, ndhJ-ndhK, clpP, psbH-petB, ycf1, and trnA-UGC-trnI-GAU, respectively. The phylogenetic trees of ten Aconitum species and other Aconitum species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among Aconitum species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of Aconitum species and an important reference and basis for Ranunculaceae species identification and phylogeny.https://www.frontiersin.org/articles/10.3389/fgene.2022.878182/fullAconitummedicinal plantschloroplast genomecomparative analysisphylogenomics |
| spellingShingle | Conglong Xia Conglong Xia Manjiong Wang Yunhui Guan Jian Li Jian Li Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships Frontiers in Genetics Aconitum medicinal plants chloroplast genome comparative analysis phylogenomics |
| title | Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships |
| title_full | Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships |
| title_fullStr | Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships |
| title_full_unstemmed | Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships |
| title_short | Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships |
| title_sort | comparative analysis of the chloroplast genome for aconitum species genome structure and phylogenetic relationships |
| topic | Aconitum medicinal plants chloroplast genome comparative analysis phylogenomics |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.878182/full |
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