Comparative genomics revealed new insights into the plastome evolution of (Onagraceae, Myrtales).

The primrose-willow ( L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including , , and . Three cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in , , and genera, with primitive IR structures in and genera. The regions , , and genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that (including , , , and ) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three species, which can be used for species identification and phylogenetic reconstruction of and Onagraceae taxa.