Plastome diversity and phylogenomic analysis of Satureja (Lamiaceae): uncovering evolutionary patterns and diagnostic markers

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Abstract
Main conclusion The chloroplast genomes of Satureja are highly conserved but contain hypervariable loci like ndhF and ycf1. These loci provide powerful molecular tools for precise species identification, phylogenetic resolution, and future conservation efforts in this important genus. Abstract The genus Satureja (Lamiaceae) comprises a valuable number of aromatic herbs and shrubs with significant ecological, medicinal, and economic value, particularly in the Mediterranean and Southwest Asia. Satureja species are renowned for their therapeutic essential oils, yet their chloroplast (cp) genomic resources remain vastly understudied, with only S. montana complete cp genome available. To address this gap, we sequenced and analyzed the complete cp genomes of three taxonomically and ecologically distinct Satureja species (S. hortensis, S. khuzestanica, and S. montana subsp. variegata) and a new individual of S. montana, using Illumina sequencing and comparative genomic approaches. The assembled cp genomes exhibited a conserved quadripartite structure, with sizes ranging narrowly from 151,777 to 151,924 bp, featuring typical large (LSC) and small (SSC) single-copy regions flanked by inverted repeats (IRs). Genome annotation revealed 128–130 genes, including core photosynthetic and ribosomal genes, with notable interspecific variation in tRNA copy numbers. Comparative analyses identified hypervariable loci (ndhF, ycf1, petN) as promising DNA barcodes for species discrimination, while codon use bias strongly favored A/T-ending codons. Simple sequence repeats (SSRs) were predominantly mononucleotide (A/T), and long repetitive sequences showed species-specific length polymorphisms. Phylogenetic reconstruction using the whole cp genomes strongly supported the monophyly of Satureja and resolved infrageneric relationships with high bootstrap confidence (> 90%), placing these species in a distinct clade sister to Thymus and Mentha. Our study provides the first comprehensive cp genomic resource for Satureja, elucidating evolutionary patterns, identifying molecular markers for taxonomy, and establishing a foundation for future conservation and biotechnological applications in this economically important genus.

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