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Rapid bursts and long-term stasis: phylogeny, evolutionary dynamics, and expression of B3 transcription factors in Arabidopsis, Cannabis, and Humulus

Year: 2026
Type: article
Abstract: The B3 superfamily is one of the largest plant transcription factor gene families, yet its evolutionary dynamics in dioecious species like Cannabis sativa remain largely unexplored. Here, we present a comprehensive phylogenetic, molecular evolution, and transcriptomic analysis of B3 domain-containing genes in Arabidopsis thaliana , C. sativa , and Humulus lupulus . Using a gene mining pipeline, we identified 110, 101, and 88 B3 genes across the five established subfamilies ( ARF , ABI3 , HSI , RAV , and REM), respectively. We identified two distinct evolutionary trajectories with the B3 superfamily. On the one hand the REM subfamily was by far the largest and characterized by massive lineage-specific tandem duplications subjected to relaxed selective constraint, suggesting distinct or partially redundant roles in reproductive development. On the other hand, specific non-tandem clades remained highly conserved under strong purifying selection. Detailed analysis of the candidate sex-determination gene CsREM16 showed low dN/dS ratios, clear one-to-one orthology across studied species, and unique persistent sex-biased expression across all six analyzed developmental stages in C. sativa . Comparative analysis of its ortholog HlREM16 confirmed a conserved female-biased expression in H. lupulus . Together, these results demonstrate a dual-mode evolutionary dynamic in the B3 superfamily and particularly in the REM genes and establish CsREM16 as a strong candidate for sex determination in C. sativa , with a potentially conserved role in H. lupulus .
DOI: 10.3389/fpls.2026.1882604
Language: English
Subfield: Plant Science
Open Access status: gold
Estimated APC paid: $3,801
OpenAlex ID: W7221914561
FWCI:
Cites: 46
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Related to: 10