Abstract: Robust phylogenies and comprehensive taxonomies are fundamental for understanding the evolution and classification of species-rich genera. Corydalis (Papaveraceae), comprising approximately 530 species, is one of the largest and most diverse angiosperm genera. While a recent classification system has been established based on phylogenomic and morphological evidence, it relied primarily on plastid genomic data, with limited consideration given to nuclear genes. Here, we compiled the genome skimming data from 411 accessions representing 265 species covering all recognized 39 sections of Corydalis. Using 6617 high quality nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs), we reconstructed a comprehensive phylogenetic framework for Corydalis. Our results strongly supported the division of Corydalis into four subgenera, including subg. Cremnocapnos, subg. Bipapillatae, subg. Sophorocapnos, and subg. Corydalis. Of the 33 sections sampled with multiple species, ten were recovered as non-monophyletic, including sect. Cheilanthifoliae, sect. Thalictrifoliae, sect. Vermiculares, sect. Rupifragae, sect. Asterostigmata, sect. Mucronatae, sect. Elatae, sect. Fasciculatae, sect. Flexuosae, and sect. Bimaculatae. Phylogenetic network analyses revealed pervasive hybridization and introgression in subg. Corydalis, suggesting that widespread hybridization and introgression are major drivers of both phylogenetic discordance and sectional non-monophyly. Our study not only provides a critical nuclear genomic perspective for Corydalis, but also offers concrete guidance for refining its infrageneric classification. In addition, our findings also underscore the necessity of future studies that integrate expanded sampling, high-quality genetic markers, and morphological data to resolve the classification of taxonomically problematic sections.

Key words: Corydalis, phylogeny, hybridization, single nucleotide polymorphism (SNP), single copy nuclear gene (SCN), monophyly