Abstract
BackgroundAlpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values.ResultsThe four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293–296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments.ConclusionsThe results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.
Highlights
Alpinia species are widely used as medicinal herbs
We reported and compared the four complete plastome sequences of A. galanga, A. nigra, A. officinarum, and A. oxyphylla sampled from Guangxi, China
The four plastomes display the typical quadripartite characters and show a high degree of conservation in organization and structure. They consist of a Large Single-Copy (LSC) region (87,267 − 88,970 bp) and a Small Single-Copy (SSC) region (15,349 − 17,908 bp), which were separated by two Inverted Repeat (IR) regions (27,490–29,951 bp) (Table 1)
Summary
Alpinia species are widely used as medicinal herbs. Zingiberaceae is the largest plant family in the order Zingiberales [1]. It contains about 1,587 species and 52 genera (The Plant List; last accessed: February 2021). The family provides essential natural resources to humans, including many useful products for food, spices, medicines, dyes, perfume, and aesthetics [2, 3]. Is the largest, most widely distributed, and most taxonomically complex genus in the Zingiberaceae, including 230 species occurring throughout tropical and subtropical Asia [4]. Many of the Alpinia species are wellknown medicinal herbs. Other Alpinia species have been widely used for bioprospection of plant essential oils for medicinal uses [5]
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