Comparative chloroplast genomics of Cousinia (Asteraceae) based on nine newly sequenced Central Asian endemic species

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.