Complete chloroplast genome of the medicinally important plant Ajuga turkestanica (Regel) Briq. (Lamiaceae) from Uzbekistan

In this study, the complete chloroplast genome sequences of Ajuga turkestanica, a perennial medicinally important herbal plant, endemic in Uzbekistan, is first reported. The next generation DNA sequencing technology was applied, providing comprehensive and valuable accurate genetic information of the chloroplast genome sequences of A. turkestanica , that facilitate species identification for its natural conservation and phylogenetic relationships within the genus-level, as well as tribal, subfamily, family levels. The whole chloroplast genome of A. turkestanica is 150,719 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 25,441 bp), separated by a small single-copy (SSC, 17,335 bp) region and a large single-copy (LSC, 82,502 bp) region. The chloroplast genome contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The GC contents is 38.2%. The repeat structure analysis detected 227 simple sequence repeats (SSRs) including the largest number of mononucleotides (127), dinucleotides (30), trinucleotides (58), tetranucleotides (11) and pentanucleotide (1) in A. turkestanica chloroplast genome. The sequence divergence analyses found seven prominent divergent regions: rps16–trnQ-UUG , trnT-UGU–trnL-UAA, ndhC– trnV-UAC, ndhF– rpl32, ndhE– ndhG, ndhF, ycf1, exhibiting a high variation level with nucleotide diversity exceeding >0.013 (Pi). The chloroplast genome structure analysis at the four genomic boundary regions (LSC/IRa, LSC/IRb, SSC/IRa, and SSC/IRb) across Ajugoideae species showed dynamic changes. The phylogenetic analysis of 38 Lamiaceae species based on utilizing chloroplast genomes has shown effectively enhance phylogenetic resolution. The results clearly prove the belonging A. turkestanica to genus Ajuga within tribe Ajugeae tribe. The situation of A. turkestanica suggests the genetic isolation within Ajuga genus, due to high level of its endemism. The complete chloroplast genomes can be used as a super-barcode to identify Ajuga species.

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