Genome-wide cyclin gene evolution in Arabidopsis and Brassica reveals polyploidization-driven duplication and flowering-time associations

Cyclin genes are plant cell cycle regulators that play essential roles in growth, development, and reproduction. However, the evolutionary dynamics and genomic organization of cyclin genes across the Brassicaceae family remain poorly understood, particularly in the context of allotetraploid genome evolution. Here, we investigated the diversity, expansion mechanisms, and potential functional diversification of cyclin genes across ten Brassicaceae genomes, including four Arabidopsis and six Brassica species. A total of 1087 cyclin genes representing 23 cyclin types were identified. Comparative genomic analyses revealed that cyclin gene expansion was strongly influenced by polyploidization in Brassica species, with 1845 duplication events involving 1063 genes. Whole-genome duplication was the predominant mechanism driving expansion, while both inter- and intra-genomic duplications contributed to gene retention in tetraploid Brassica species, with the highest duplication frequency observed in Brassica juncea. Across genomes, 120 physical gene clusters were identified, including homogeneous and heterogeneous types. Ortholog analysis between progenitor and allotetraploid species identified 852 orthologous pairs involving 366 genes, indicating extensive conservation following allotetraploid formation. Phylogenetic analysis resolved cyclins into three major clades, while expression-based clustering in Brassica napus grouped genes into four major clusters, suggesting functional diversification. Integration of pan-genomic and flowering-time QTL analyses further identified two cyclin genes, Bna21cycA2 and Bna113cycD4, which contain amino acid polymorphisms and represent putative candidate variations potentially associated with flowering-time variation across multiple genomes. These findings provide new insights into the evolutionary expansion, retention, and potential functional divergence of cyclin genes in Brassicaceae and highlight candidate loci for future functional studies and crop improvement.