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Background  Crape myrtles, belonging to the genus  Lagerstroemia  L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping and gardening. However, the phylogenetic relationships within  Lagerstroemia  have remained unresolved likely caused by limited sampling and the insufficient number of informative sites used in previous studies.    Results  In this study, we sequenced 20  Lagerstroemia  chloroplast genomes and combined with 15 existing chloroplast genomes from the genus to investigate the phylogenetic relationships and divergence times within  Lagerstroemia . The phylogenetic results indicated that this genus is a monophyletic group containing four clades. Our dating analysis suggested that  Lagerstroemia  originated in the late Paleocene (~ 60 Ma) and started to diversify in the middle Miocene. The diversification of most species occurred during the Pleistocene. Four variable loci,  trnD-trnY-trnE ,  rrn16-trnI, ndhF-rpl32-trnL  and  ycf1 , were discovered in the  Lagerstroemia  chloroplast genomes.    Conclusions  The chloroplast genome information was successfully utilized for molecular characterization of diverse crape myrtle samples. Our results are valuable for the global genetic diversity assessment, conservation and utilization of  Lagerstroemia.Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07769-x.

Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)