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 plastome sequences and nuclear ribosomal ITS data. The assembled plastomes were highly uniform in size (approximately 152 kb), displayed the canonical 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 sixteen plastomes 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 complete plastome data did not consistently recover morphologically defined sections as monophyletic, whereas the ITS 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 plastid and nuclear signals and indicate that certain infrageneric classifications within Cousinia warrant re-evaluation

Cousinia (Asteraceae, Cardueae) is one of the most diverse genera of the Irano–Turanian floristic region, but relationships among its species remain insufficiently resolved. In this study, nine complete chloroplast genomes of Cousinia species endemic to the Pamir–Alay mountain system were sequenced and analyzed together with previously published plastomes and nuclear ribosomal ITS data. The newly assembled plastomes were approximately 152 kb in length, exhibited a typical quadripartite structure, and had a GC content of 37.7%. Gene content was highly conserved, with 131 annotated genes in most species. Codon usage analysis of 16 plastomes showed a consistent preference for A/T-ending codons. Sliding-window analysis indicated low overall nucleotide diversity (Pi = 0–0.00918), with several variability hotspots located mainly in the large and small single-copy regions. A total of eleven types of simple sequence repeats were detected, of which A/T mononucleotide repeats were the most abundant. Phylogenetic analyses based on complete chloroplast genomes did not fully support the monophyly of morphologically defined sections, whereas ITS data provided better resolution of sectional boundaries. Morphological examination of anther appendages identified nine distinct structural groups and revealed patterns partly consistent with molecular results, suggesting the need for further taxonomic revision in some sections of Cousinia.

Fritillaria yakutii (Liliaceae), from the Babatag Range in Surkhandarya, Uzbekistan, is described as new. It belongs to Fritillaria subgenus Rhinopetalum, which is known for its recent diversification and morphological variation across Central Asia. Morphologically, F. yakutii closely resembles F. bucharica and F. baisunensis but differs in key floral characteristics, including the color and pattern of the perianth and anthers. Phylogenetic analyses based on complete chloroplast genome sequences confirms its placement within the Rhinopetalum clade, forming a strongly supported sister relationship with F. bucharica, F. gibbosa and F. baisunensis. The chloroplast genome of F. yakutii has a total length of 151,757 bp and contains 130 annotated genes, including 84 protein-coding genes. The species is currently known only from its type locality, where approximately 300 mature individuals were recorded in 2020. Given the limited available data on its distribution and population trends, F. yakutii is assessed as Data Deficient (DD) under the IUCN Red List criteria.