Abstract
Abstract Chloroplast genomes of angiosperms exhibit a high degree of structural and sequence conservation, making them valuable resources for phylogenetic and systematic studies. However, the genus Corydalis (Papaveraceae), comprising more than 540 species worldwide, is characterized by a complex infrageneric structure and extensive structural rearrangements within the chloroplast genome, posing significant challenges for taxonomic classification. In the present study, we conducted a comparative analysis of chloroplast DNA sequences from five poorly studied Corydalis species native to the flora of Kazakhstan: Corydalis ledebouriana Kar. & Kir., C. glaucescens Regel, C. sewerzowii Regel, C. schanginii (Pall.) B. Fedtsch., and C. gortschakovii Schrenk. The chloroplast markers trnL intron and atpB–rbcL intergenic spacer were employed to assess both interspecific variation and the conservation of sequences within taxonomic sections. Flow cytometric analysis revealed a broad range of genome sizes and ploidy levels among the investigated species. Corydalis gortschakovii, assigned to the subgenus Capnoides, was the only diploid species, exhibiting the smallest genome size and high measurement stability, consistent with its basal and evolutionarily isolated position within the genus. In contrast, C. schanginii exhibited a tetraploid genome with partial reduction of the monoploid genome size. Species belonging to the sections Pes-gallinaceus and Leonticoides (C. glaucescens, C. ledebouriana, and C. sewerzowii) were characterized by large genomes and high ploidy levels (6×–8×), indicating a close evolutionary relationship and highlighting the important role of polyploidization in their diversification. Phylogenetic analyses based on the trnL–trnF and atpB–rbcL chloroplast regions supported the division of the studied species into the two subgenera, Capnoides and Capnites, and confirmed the monophyly of the sections Leonticoides and Pes-gallinaceus. Corydalis gortschakovii formed a distinct basal lineage, whereas the polyploid species exhibited strong genetic coherence within sections and robust sister-group relationships. Comparison of the two chloroplast markers demonstrated their complementary phylogenetic utility: the atpB–rbcL region provided superior resolution of deeper phylogenetic nodes, whereas the trnL–trnF region was more sensitive in detecting variation at the sectional level. These findings highlight the value of integrating cytogenetic and chloroplast genomic data for resolving phylogenetic relationships within Corydalis, identifying ploidy variation, and improving our understanding of the evolutionary processes shaping the genus, including polyploidization and structural genome rearrangements. The results provide a robust framework for future integrative studies incorporating broader geographic sampling and expanded taxonomic coverage.