Objective China is the modern distribution and differentiation center of Spiraea plants. S. media and S. pubescens are sympatric species of Spiraea distributed in the forest-grass transition zone of Inner Mongolia, northern China. Analysis of chloroplast genomic differences between the two species can provide a basis for identifying plant relatives in the same genus.

Method In this study, the complete chloroplast genome sequences of the two species were obtained by assembly and annotation using second-generation sequencing technology and Illumina Novaseq 6000 platform, and the sequence structures were analyzed using bioinformatics methods to construct phylogenetic trees.

Result The total length of chloroplast genome of S. media was 155 916 bp with 36.72% total GC content, and the total length of chloroplast genome of S. pubescens was 155 942 bp with 36.76% total GC content. Both were annotated to obtain 130 genes, 111 of which were unique, containing 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. S. media and S. pubescens detected 238 and 241 simple repeats, respectively, with codon preference ending in A or U over codon preference ending in G or C and the genomic variation regions were mainly distributed in non-coding regions. They were both with the largest number of codons encoding leucine and the least number of codons encoding cysteine. The phylogenetic tree showed that these two species formed a sister group, and had a relatively close relation. Spiraea and Sibiraea were closely related, showing a sister group relationship.

Conclusion The results of the study can provide basic information for the phylogeny, taxonomic identification and resource development and utilization of Spiraea.