English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Background   Alpinia  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.    Results  The 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 ( acc D and  ycf 1) 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:  pet N- psb M and  psa J- rpl 33, respectively. The discrimination success rate was 100 % in validation experiments.    Conclusions  The 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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03204-1.

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences