Genome-wide Analysis of Core Histone Genes and Expression Dynamics of the H3 subfamily in Brassica napus

This study performed a comprehensive genome-wide identification and phylogenetic analysis of the core histone family (CHF) in Arabidopsis thaliana , Brassica napus , and its two diploid progenitor species, Brassica rapa and Brassica oleracea . Using bioinformatics approaches, a total of 86 core histone genes were identified in B. napus , classified into four subfamilies—H2A, H2B, H3, and H4. Comparative analyses revealed that histone H4 is highly conserved across the five studied species, whereas the H2A and H2B subfamilies exhibit substantial sequence divergence. In B. napus , genes derived from the C genome (originating from B. oleracea ) show a higher retention rate compared to those originating from the A genome (from B. rapa ). Promoter regions of the core histone genes are enriched with 21 distinct functional cis-regulatory elements, many of which are associated with a "light–hormone–stress" regulatory network. Furthermore, the centromere-specific histone variant CENH3 was found to localize to the nucleus and forms a distinct clade in the phylogenetic tree, indicating its divergent evolutionary trajectory. These findings provide a solid theoretical foundation for understanding the evolutionary dynamics of histone gene families within the Brassicaceae family.