Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert
Background: Geoffroea decorticans is a vulnerable native species inhabiting the Atacama Desert. Here, we describe the structure, gene composition and phylogeny of the complete chloroplast genome of this legume species. Results: The chloroplast genome consisted of 158,399 bp, with typical quadriparti...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | Electronic Journal of Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0717345822000392 |
| _version_ | 1817986385495195648 |
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| author | Roberto Contreras-Díaz Felipe S. Carevic Wilson Huanca-Mamani Rómulo Oses Mariana Arias-Aburto María Navarrete-Fuentes |
| author_facet | Roberto Contreras-Díaz Felipe S. Carevic Wilson Huanca-Mamani Rómulo Oses Mariana Arias-Aburto María Navarrete-Fuentes |
| author_sort | Roberto Contreras-Díaz |
| collection | DOAJ |
| description | Background: Geoffroea decorticans is a vulnerable native species inhabiting the Atacama Desert. Here, we describe the structure, gene composition and phylogeny of the complete chloroplast genome of this legume species. Results: The chloroplast genome consisted of 158,399 bp, with typical quadripartite structures: a large single copy (88,081 bp), a small single copy (18,976 bp), and two inverted repeats (25,671 bp). Geoffroea decorticans chloroplast genome was similar in size and gene number to that of G. spinosa, but it was slightly different in structure. Complete chloroplast analysis of G. decorticans revealed 129 genes, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene (rpl22). In G. decorticans, the rps16 gene showed a deletion, which led to a premature stop codon, probably causing loss of functionality. Phylogenetic analysis of 20 complete chloroplast genomes confirmed the placement to G. decorticans within the Pterocarpus clade. Conclusions: In this study, we report the complete chloroplast genome of Geoffroea decorticans for the first time, which can be used for phylogenetic studies and reconstruction of the biogeography history of the genus Geoffroea in South America.How to cite: Contreras-Díaz R, Carevic FS, Huanca-Mamani W, et al. Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.005. |
| first_indexed | 2024-04-14T00:09:33Z |
| format | Article |
| id | doaj.art-6adbbdde94a24060b82b4021984d8f93 |
| institution | Directory Open Access Journal |
| issn | 0717-3458 |
| language | English |
| last_indexed | 2024-04-14T00:09:33Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Electronic Journal of Biotechnology |
| spelling | doaj.art-6adbbdde94a24060b82b4021984d8f932022-12-22T02:23:24ZengElsevierElectronic Journal of Biotechnology0717-34582022-11-01601925Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama DesertRoberto Contreras-Díaz0Felipe S. Carevic1Wilson Huanca-Mamani2Rómulo Oses3Mariana Arias-Aburto4María Navarrete-Fuentes5Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copayapu 485, 1530000 Copiapó, Chile; Corresponding authorLaboratorio de Ecología Vegetal, Facultad de Recursos Naturales Renovables. Universidad Arturo Prat, Campus Huayquique, 1100000 Iquique, ChileLaboratorio de Biología Molecular de Plantas, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, 1000000 Arica, ChileCentro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copayapu 485, 1530000 Copiapó, ChileCentro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copayapu 485, 1530000 Copiapó, ChileCentro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copayapu 485, 1530000 Copiapó, ChileBackground: Geoffroea decorticans is a vulnerable native species inhabiting the Atacama Desert. Here, we describe the structure, gene composition and phylogeny of the complete chloroplast genome of this legume species. Results: The chloroplast genome consisted of 158,399 bp, with typical quadripartite structures: a large single copy (88,081 bp), a small single copy (18,976 bp), and two inverted repeats (25,671 bp). Geoffroea decorticans chloroplast genome was similar in size and gene number to that of G. spinosa, but it was slightly different in structure. Complete chloroplast analysis of G. decorticans revealed 129 genes, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene (rpl22). In G. decorticans, the rps16 gene showed a deletion, which led to a premature stop codon, probably causing loss of functionality. Phylogenetic analysis of 20 complete chloroplast genomes confirmed the placement to G. decorticans within the Pterocarpus clade. Conclusions: In this study, we report the complete chloroplast genome of Geoffroea decorticans for the first time, which can be used for phylogenetic studies and reconstruction of the biogeography history of the genus Geoffroea in South America.How to cite: Contreras-Díaz R, Carevic FS, Huanca-Mamani W, et al. Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.005.http://www.sciencedirect.com/science/article/pii/S0717345822000392Atacama DesertChloroplast genomeDalbergieaeGeoffroea decorticansLegumeNative tree |
| spellingShingle | Roberto Contreras-Díaz Felipe S. Carevic Wilson Huanca-Mamani Rómulo Oses Mariana Arias-Aburto María Navarrete-Fuentes Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert Electronic Journal of Biotechnology Atacama Desert Chloroplast genome Dalbergieae Geoffroea decorticans Legume Native tree |
| title | Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert |
| title_full | Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert |
| title_fullStr | Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert |
| title_full_unstemmed | Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert |
| title_short | Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert |
| title_sort | chloroplast genome structure and phylogeny of geoffroea decorticans a native tree from atacama desert |
| topic | Atacama Desert Chloroplast genome Dalbergieae Geoffroea decorticans Legume Native tree |
| url | http://www.sciencedirect.com/science/article/pii/S0717345822000392 |
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