Journal Article

The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family

Pan, Kun, Wei, Na, Yuan, Lin, Tang, Tianle, Gao, Bingmiao, Hou, Jie

2019

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Acclimatization - genetics / Adaptation / Alpinia / Alpinia - genetics / ATP synthase / Base Composition / Bioinformatics / Biology and Life Sciences / China / Chinese herbal medicine / Chloroplasts / Chromosome Mapping / Comparative analysis / Computer and Information Sciences / Deoxyribonucleic acid / DNA / DNA, Chloroplast - genetics / DNA, Plant - genetics / Drugs, Chinese Herbal / Engineering and Technology / Evolution & development / Evolution, Molecular / Genes / Genetic diversity / Genome, Chloroplast / Genome, Plant / Genomes / Genomics / Herbal medicine / Laboratories / Microsatellite Repeats / NADH / Nicotinamide adenine dinucleotide / Nucleotide sequence / Organelles / Pharmacy / Photosystem II / Phylogenetics / Phylogeny / Plant sciences / Plants, Medicinal - genetics / Research and Analysis Methods / Simple sequence repeats / Zingiberaceae / Zingiberaceae - classification / Zingiberaceae - genetics