A chloroplast genomic dataset for accurate identification of the endangered Lagerstroemia minuticarpa Debb. ex P. C. Kanjilal

Lagerstroemia minuticarpa Debb. ex P. C. Kanjilal is a deciduous tree listed as a nationally protected wild plant (level II) in China. The complete chloroplast genome of L. minuticarpa was sequenced using the DNBSEQ-T7 platform. The genome is 152,183 bp in length and exhibits a typical quadripartite structure, consisting of a large single-copy (LSC) region of 84,009 bp, a small single-copy (SSC) region of 16,924 bp, and a pair of inverted repeats (IRs) of 25,625 bp each. It contains 133 genes in total, including 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content of the genome is 37.31%. Phylogenetic analysis based on 39 chloroplast genomes revealed that L. minuticarpa forms an independent lineage nested within the genus Lagerstroemia . Additionally, pairwise alignment identified ten highly variable chloroplast loci (including both coding and intergenic regions) with elevated parsimony-informative sites, which hold promise as specific DNA barcodes for species identification in Lagerstroemia . These data enrich the genetic knowledge of Lagerstroemia species in the Lythraceae family and provide a basis for further research in molecular identification, genetic breeding, and other related fields.