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New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales)
Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10655658/ https://www.ncbi.nlm.nih.gov/pubmed/38020533 http://dx.doi.org/10.1177/11769343231210756 |
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author | Nhat Nam, Nguyen Hoang Danh, Nguyen Minh Thiet, Vu Do, Hoang Dang Khoa |
author_facet | Nhat Nam, Nguyen Hoang Danh, Nguyen Minh Thiet, Vu Do, Hoang Dang Khoa |
author_sort | Nhat Nam, Nguyen |
collection | PubMed |
description | Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa. |
format | Online Article Text |
id | pubmed-10655658 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-106556582023-11-15 New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) Nhat Nam, Nguyen Hoang Danh, Nguyen Minh Thiet, Vu Do, Hoang Dang Khoa Evol Bioinform Online Original Research Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa. SAGE Publications 2023-11-15 /pmc/articles/PMC10655658/ /pubmed/38020533 http://dx.doi.org/10.1177/11769343231210756 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by-nc/4.0/This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Original Research Nhat Nam, Nguyen Hoang Danh, Nguyen Minh Thiet, Vu Do, Hoang Dang Khoa New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title | New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title_full | New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title_fullStr | New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title_full_unstemmed | New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title_short | New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales) |
title_sort | new insights into the evolution of chloroplast genomes in ochna species (ochnaceae, malpighiales) |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10655658/ https://www.ncbi.nlm.nih.gov/pubmed/38020533 http://dx.doi.org/10.1177/11769343231210756 |
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