Sequence structure and phylogenetic analysis of the chloroplast genomes of Alangium chinense (Lour.) Harms and its different subspecies

Alangium chinense is a commonly used medicinal plant of Alangiaceae Alangium, one of the characteristic Miao medicines in Guizhou. The genus is strongly differentiated and has complex morphological variation, with significant differences in active ingredients and potency among herbs. In this paper, we sequenced the chloroplast genomes of Alangium chinense subsp. Pauciflorum, Alangium chinense subsp. Strigosum and Alangium kurzii Craib using Illumina high-throughput sequencing technology. The genomes of Alangium chinense subsp. Pauciflorum, Alangium chinense subsp. Strigosum and Alangium kurzii Craib chloroplasts were sequenced, their assembly annotation and structural characterization were completed, and the genomes of the congeners Alangium chinense and Alangium alpinum were downloaded from NCBI for comparative analysis. Finally, the phylogenetic tree was constructed by selecting published species with close affinity to Alangium chinense family from NCBI. The results were as follows: Alangium chinense subsp. Pauciflorum, Alangium chinense subsp. Strigosum and Alangium kurzii Craib chloroplast genomes were 156 670, 156 672 and 156 871 bp in length, with a typical four-segment structure, all containing one long single copy region (LSC), one short single copy region (SSC) and two inverted repeat regions (IRa and IRb). All of them were annotated to 133 genes, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Three types of long repeat sequences and SSR loci, forward repeats, palindrome repeats and reverse repeats, were found in all chloroplast genomes. Comparative genomic analysis showed that there was diversity in the boundary transition regions of the five species, no rearrangements or inversions were found in the chloroplast genome, and there were significant differences in the coding regions of ndhA, ycf1, rpl16, ycf2, and petD genes, which provided new loci for molecular identification of Patagonia. In the phylogenetic analysis, Alangium kurzii var. kurzii clustered as a single species, and Alangium chinense subsp. Pauciflorum and Alangium chinense subsp. Strigosum clustered as a single species, with a support rate of 93 and close affinity, indicating that the phylogenetic tree can be used for the species identification. This paper can provide a basis for the taxonomic identification of Alangium, ensure the safety of clinical use of anise herbs and regulate the market of Alangium chinense herbs.