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In this study, we assembled and annotated the chloroplast (cp) genome of the  Euonymus  species  Euonymus fortunei ,  Euonymus phellomanus , and  Euonymus maackii , and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the  Euonymus  cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of  Euonymus  happened expanding resulting that the  rps19  entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among  Euonymus . The simple-sequence repeats (SSRs) of  Euonymus  species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus  Euonymus . Signatures of positive selection were seen in  rpoB  protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of  Euonymus  and related species, the results of which were consistent with traditional taxonomic classifications. It showed that  E. fortunei  sister to the  Euonymus japonicus , whereby  E. maackii  appeared as sister to  Euonymus hamiltonianus . Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of  Euonymus  species.

frontiers in plant science

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae