Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis.

Yue Zhang,Zhong-Lian Zhang,Hui-Fang Sun,An-Shun Xu,Cui-Yun Yin,Li-Xia Zhang,Dei-Ying Tang,Yao Li,Mei-Fang Song

doi:10.3389/fpls.2021.705892

Yue Zhang, Zhong-Lian Zhang + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2021.705892

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Abstract

Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine–cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.

Highlights

Alpinia Roxb. is an important genus of Zingiberaceae and includes 250 species mainly distributed in tropical Southeast Asia, but their distribution extends south into Australia and the South Pacific islands, and west into India
The whole CP genomes contain a pair of IRs (IRa and IRb) at, respectively, 27,313 and 29,705 bp separated by an small single-copy (SSC) region at 17,909 and 15,181 bp, and a large single-copy (LSC) region at 87,565 and 87,732 bp
The distribution of genes in the two CP genomes is the same: 81 genes are distributed in the LSC region, including 60 protein-coding genes and 21 tRNA genes, whereas the SSC region contains 11 protein-coding genes and one tRNA gene; a total of 20 genes are duplicated in the IR regions, including eight protein-coding genes, eight tRNA genes, and four rRNAs (Figure 1 and Supplementary Table 2)

Summary

Introduction

Alpinia Roxb. is an important genus of Zingiberaceae and includes 250 species mainly distributed in tropical Southeast Asia, but their distribution extends south into Australia and the South Pacific islands, and west into India Alpinia oxyphylla is an important food and traditional Chinese herbal medicine; previous studies have demonstrated its antioxidative, antiinflammatory, anti-apoptotic, and neuropharmacological effects (Zhang et al, 2011; Gao et al, 2019; Li J. et al, 2020). A. galanga and A. zerumbet have been used as traditional medicines and food seasonings for hundreds of years (Chouni and Paul, 2018; Xiao et al, 2020). Modern pharmacological research has shown that A. zerumbet has important physiological and pharmacological functions, including antioxidative, antimicrobial, antianxiety effects, and promotes osteoblastic cell differentiation activities (Elzaawely et al, 2007; Sousa et al, 2015; Kumagai et al, 2016; Xuan et al, 2016; Castro et al, 2018). These problems have severely hindered the clinical use of and scientific research related to medicinal Alpinia species

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