Rapid bursts and long-term stasis: phylogeny, evolutionary dynamics, and expression of B3 transcription factors in Arabidopsis, Cannabis, and Humulus
- 1School of Biology and Environmental Science and Earth Institute, University College Dublin
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 .
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BibTeX
@article{toscani2026rapid,
title = {{Rapid bursts and long-term stasis: phylogeny, evolutionary dynamics, and expression of B3 transcription factors in Arabidopsis, Cannabis, and Humulus}},
author = {Matteo Toscani and Ainhoa Riera-Begue and Nina Trubanová and Susanne Schilling and Rainer Melzer},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1882604},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1882604/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Rapid bursts and long-term stasis: phylogeny, evolutionary dynamics, and expression of B3 transcription factors in Arabidopsis, Cannabis, and Humulus
AU - Matteo Toscani
AU - Ainhoa Riera-Begue
AU - Nina Trubanová
AU - Susanne Schilling
AU - Rainer Melzer
PY - 2026
DA - 2026/10/15
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1882604
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1882604/full
AB - 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 .
SN - 1664-462X
ER -