Complete chloroplast genome of a valuable medicinal plant, Huperzia serrata (Lycopodiaceae), and comparison with its congener1

PREMISE OF THE STUDY Here we report the complete chloroplast genome of the important medicinal species Huperzia serrata (Lycopodiaceae) and compare it to the chloroplast genome of the congeneric species H. lucidula. METHODS AND RESULTS The whole chloroplast genome of H. serrata was sequenced using an Illumina platform and assembled with Geneious version R9.0.5. The genome size of H. serrata was 154,176 bp, with 36.3% GC content. The complete chloroplast genome contained 120 unique genes, including 86 coding genes, four rRNA genes, and 30 tRNA genes. Comparison with the chloroplast genome of H. lucidula revealed three highly variable regions (rps16-chlB, ycf12-trnR, and ycf1) between these two species and 252 mutation events including 27 insertion/deletion polymorphisms and 225 single-nucleotide polymorphisms (SNPs). Ninety-two SNPs were identified in the gene-coding regions. In addition, 18 microsatellite sites were found, which can potentially be used in phylogeographic studies. CONCLUSIONS The complete chloroplast genome of H. serrata is reported here, and will be a valuable genome resource for further phylogenetic, evolutionary, and medical studies of medicinal plants in the genus Huperzia.