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Lagerstroemia  (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for  Lagerstroemia  are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of  Lagerstroemia fauriei . To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of  L .  fauriei  and several other Lythraceae species lack the  rpl2  intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of  L .  fauriei  provides a much needed genetic resource for further phylogenetic research in  Lagerstroemia  and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)