Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

( ), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of was generated via the genome skimming approach and compared to another available cp genome comprehensively at the genome scale. We found that the structure of the cp genome in was highly consistent with genome size variation which might result from DNA repeat variations in the two cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of . Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between and in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.