Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae)
To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome se...
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| Published in | PloS one Vol. 18; no. 6; p. e0286587 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
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01.06.2023
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| Abstract | To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H. forbesii QX (157,181 bp), H. forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atpF-atpH, petD, and rps15-ycf1. Phylogenetic analysis showed that H. forbesii LQ and H. forbesii WQ were closely related, followed by H. forbesii QX. This study showed that the three varieties of H. forbesii could be identified by the complete cp genome and specific DNA barcode (trnC-GCA-petN) and provided a new idea for germplasm identification of similar cultivated varieties. |
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| AbstractList | To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H. forbesii QX (157,181 bp), H. forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atpF-atpH, petD, and rps15-ycf1. Phylogenetic analysis showed that H. forbesii LQ and H. forbesii WQ were closely related, followed by H. forbesii QX. This study showed that the three varieties of H. forbesii could be identified by the complete cp genome and specific DNA barcode (trnC-GCA-petN) and provided a new idea for germplasm identification of similar cultivated varieties. To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H . forbesii QX (157,181 bp), H . forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atp F- atp H, pet D, and rps 15- ycf 1. Phylogenetic analysis showed that H . forbesii LQ and H . forbesii WQ were closely related, followed by H . forbesii QX. This study showed that the three varieties of H . forbesii could be identified by the complete cp genome and specific DNA barcode ( trn C-GCA- pet N) and provided a new idea for germplasm identification of similar cultivated varieties. To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H . forbesii QX (157,181 bp), H . forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atp F- atp H, pet D, and rps 15- ycf 1. Phylogenetic analysis showed that H . forbesii LQ and H . forbesii WQ were closely related, followed by H . forbesii QX. This study showed that the three varieties of H . forbesii could be identified by the complete cp genome and specific DNA barcode ( trn C-GCA- pet N) and provided a new idea for germplasm identification of similar cultivated varieties. |
| Audience | Academic |
| Author | Dong, Shengjian Zhirong, Sun Zhu, Chenghao Jiang, Yuan Bai, Yu |
| AuthorAffiliation | 2 College of Applied Technology, Gansu Agricultural University. Lanzhou, Gansu, China 1 School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China Texas A&M University and Texas A&M Agrilife Research, UNITED STATES |
| AuthorAffiliation_xml | – name: Texas A&M University and Texas A&M Agrilife Research, UNITED STATES – name: 2 College of Applied Technology, Gansu Agricultural University. Lanzhou, Gansu, China – name: 1 School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China |
| Author_xml | – sequence: 1 givenname: Chenghao surname: Zhu fullname: Zhu, Chenghao organization: School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China – sequence: 2 givenname: Yuan surname: Jiang fullname: Jiang, Yuan organization: School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China – sequence: 3 givenname: Yu surname: Bai fullname: Bai, Yu organization: School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China – sequence: 4 givenname: Shengjian surname: Dong fullname: Dong, Shengjian organization: College of Applied Technology, Gansu Agricultural University. Lanzhou, Gansu, China – sequence: 5 givenname: Sun orcidid: 0000-0002-6698-4773 surname: Zhirong fullname: Zhirong, Sun organization: School of Chinese Materia Medica, Beijing University of Chinese Medicine. Beijing, Beijing, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37262084$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright: © 2023 Zhu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. COPYRIGHT 2023 Public Library of Science 2023 Zhu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2023 Zhu et al 2023 Zhu et al 2023 Zhu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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| Snippet | To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp)... To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp)... |
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| SubjectTerms | Analysis Apiaceae Biology and Life Sciences Biotechnology Chinese medicine Chloroplasts Comparative studies Computer and Information Sciences Control Deoxyribonucleic acid DNA Endangered species Engineering and Technology Gene sequencing Genes Genetic aspects Genetic engineering Genetic testing Genomes Genomics Germplasm Identification and classification Phylogenetics Phylogeny Protection and preservation Research and Analysis Methods |
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| Title | Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae) |
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