Structural Characterization of Chloroplast Genome in Alpinia japonica (Thunb.) Miq., a Medicinal Plant of the Genus Alpinia.

The analysis of chloroplast gene characteristics in Alpinia japonica (Thunb.) Miq. is of great significance for developing relevant genetic resources. The high-throughput sequencing and bioinformatic research were performed to analyze the chloroplast genome characteristics of A. japonica. The total chloroplast genome length of A. japonica was 161,906 bp, with a typical circular tetrameric structure. And 133 genes were annotated, comprising 87 protein-coding, 38 tRNA, and 8 rRNA genes. Furthermore, 22 genes contained two copies, and 18 genes owned introns. Repeat sequence analysis showed that it contains 321 simple sequence repeats (SSRs) and 37 long segment repeats. Compared with the chloroplast genomes of eight representative plants in the genus Alpinia , the gene structure, type, and quantity were relatively conservative. Rps12 was the highest variation site in the entire chloroplast gene. A phylogenetic tree showed that the genus Alpinia was the most closely related to the genus Amomum. Meanwhile, A. japonica is the most closely related to Alpinia chinensis belonging to the genus Alpinia. Overall, the chloroplast genome of a new species was reported in the genus Alpinia , and a basis was provided for the utilization of Alpinia plants as a medical resource. [ABSTRACT FROM AUTHOR]