توالي‌يابي، تحليل مقايسه‌اي و مطالعه فيلوژنتيكي ژنوم كلروپلاست گونه‌هاي Stachys persica و Stachys germanica

The genus Stachys, a large an‎d taxonomically intricate group within the Lamiaceae family, includes numerous species valued in traditional medicine, yet their evolutionary relationships are often obscured by morphological complexity. To address these systematic challenges, this study aimed to generate essential genomic resources for two medicinally important species, S. persica an‎d S. germanica, an‎d to employ them for resolving phylogenetic relationships, identifying informative DNA barcodes, an‎d uncovering genomic signatures of evolution. We therefore extracted high-quality total DNA from fresh leaf tissue an‎d sequenced the complete chloroplast (cp) genomes on an Illumina HiSeq platform. Following quality filtering, the genomes were de novo assembled using GetOrganelle an‎d annotated with a combination of CPGAVAS2 an‎d GeSeq. These new genomes were then subjected to a detailed comparative analysis against seven other congeneric species, investigating genome structure, codon usage via Relative Synonymous Codon Usage (RSCU) values, simple sequence repeat (SSR) distribution, nucleotide diversity (Pi) calculated via sliding window analysis in CPStools, an‎d signatures of positive selec‎tion using site-specific models in EasyCodeML Our findings revealed highly conserved, quadripartite genomes, with interspecific variation arising from shifts at inverted repeat boundaries an‎d a concentration of SSRs in non-coding regions. Critically, sliding window analysis identified hypervariable regions, such as the trnL-trnF intergenic spacer an‎d the matK an‎d ycf1 genes, as promising can‎didate DNA barcodes for species discrimination. Additionally, selec‎tion pressure analysis identified specific codons within the petB gene as under positive selec‎tion. Finally, a maximum likelihood phylogenetic tree was reconstructed in IQ-TREE using the concatenated sequence of all protein-coding genes, with node support assessed via ultrafast bootstrapping. This phylogenomic framework provided robust resolution, confirming Stachys monophyly an‎d precisely placing S. germanica as sister to S. byzantina, with S. persica as their closest relative. Importantly, comparative phylogenetic tests of individual barcode loci (matK, ycf1, rpl16) confirmed the superior resolving power of the whole-genome data. In conclusion, this study provides foundational chloroplast genomes for S. persica an‎d S. germanica, delivering a resolved phylogeny, can‎didate molecular markers for identification, an‎d insights into the genomic evolution of this valuable genus.

ابوذر سورني

مجيد طالبي , محمد مهدي مجيدي