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Teucrium  is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of  T. stocksianum  subsp.  stenophyllum  R.A.King (TSS),  T. stocksianum  subsp.  stocksianum  Boiss. (TS) and  T. mascatense  Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae ( Ajuga reptans  L.,  Caryopteris mongholica  Bunge,  Lamium album  L.,  Lamium galeobdolon  (L.) Crantz, and  Stachys byzantina  K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψ rps19  was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the  pbsA  gene was present in the LSC at varying distances from the J LA  (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus  Teucrium  and its subspecies that may be applied to a more comprehensive study.

Complete chloroplast genomes of medicinally importantTeucriumspecies and comparative analyses with related species from Lamiaceae