Comparative Analysis of the Chloroplast Genome for Species: Genome Structure and Phylogenetic Relationships

is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 () to 155,921 bp (), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 () to 132 (. ), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 chloroplast genomes, including ten chloroplast genomes and other sequenced species. A total of 48-79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including ---, , -, , -, , and ---, respectively. The phylogenetic trees of ten species and other species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of species and an important reference and basis for Ranunculaceae species identification and phylogeny.