Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

作者：Yang Yu, Yuwei Han, Yingmei Peng, Zunzhe Tian, Peng Zeng, Hang Zong, Tinggan Zhou, Jing Cai · 发表于：Chinese Medicine · 年份：2021 · DOI：10.1186/s13020-021-00538-8 · 被引用次数：18 · 研究领域：Genomics and Phylogenetic Studies、Wood and Agarwood Research、Plant Diversity and Evolution

BACKGROUND: In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. METHODS: In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. RESULTS: The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgro...