Abstract
Cousinia (Asteraceae: Cardueae) represents one of the most species-rich genera within the Irano-Turanian floristic region, yet interspecific relationships remain incompletely resolved. Here, nine chloroplast genomes from species endemic to the Pamir-Alay mountain system were newly sequenced and analyzed in combination with previously published complete chloroplast (cp) genome sequences and nuclear ribosomal DNA (nrDNA) data. The assembled cp genomes were highly uniform in size (approximately 152 kb), displayed the quadripartite organization of angiosperm chloroplasts, and possessed a GC content of 37.7%. Gene composition was largely conserved, with 131 annotated genes identified in most taxa. Examination of synonymous codon usage across 16 cp genomes revealed a consistent bias toward A/T-ending codons. Sliding-window analysis demonstrated generally low nucleotide diversity (Pi = 0-0.00918), although several divergence hotspots were detected, primarily within the large and small single-copy regions. Eleven categories of simple sequence repeats were identified, with A/T-rich mononucleotide motifs predominating. Phylogenetic reconstruction based on cp genomes data did not consistently recover morphologically defined sections as monophyletic, whereas the nrDNA dataset provided improved resolution of sectional delimitations. Comparative analysis of anther appendage morphology recognized nine structural groups and showed partial congruence with molecular evidence. Together, these findings highlight incongruence between chloroplast and nuclear signals and indicate that certain infrageneric classifications within Cousinia warrant re-evaluation.