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The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family.
- Source :
-
PloS one [PLoS One] 2019 Jun 24; Vol. 14 (6), pp. e0218817. Date of Electronic Publication: 2019 Jun 24 (Print Publication: 2019). - Publication Year :
- 2019
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Abstract
- Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Acclimatization genetics
Base Composition
China
Chromosome Mapping
DNA, Chloroplast genetics
DNA, Plant genetics
Drugs, Chinese Herbal
Evolution, Molecular
Microsatellite Repeats
Phylogeny
Zingiberaceae classification
Alpinia genetics
Genome, Chloroplast
Genome, Plant
Plants, Medicinal genetics
Zingiberaceae genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 14
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 31233551
- Full Text :
- https://doi.org/10.1371/journal.pone.0218817