# The WAK/WAKL gene family in Phaseolus vulgaris: genomic characterization and expression under Colletotrichum lindemuthianum infection

## TL;DR

This paper studies the WAK/WAKL gene family in common bean to understand how genetic variation relates to resistance against a fungal disease.

## Contribution

The study provides a comprehensive genomic and transcriptomic characterization of WAK/WAKL genes in Phaseolus vulgaris under infection.

## Key findings

- Twenty-five distinct domains were identified in PvWAKs and PvWAKLs, indicating modular diversification.
- Differential expression of PvWAK/WAKL genes was observed in resistant and susceptible bean cultivars over time.
- Candidate genes linked to anthracnose resistance were prioritized based on structural and expression data.

## Abstract

Wall-associated kinases (WAKs) and WAK-like proteins (WAKLs) are receptor-like kinases implicated in plant perception of extracellular cues and immune signaling. In common bean (Phaseolus vulgaris), differential resistance to Colletotrichum lindemuthianum offers an opportunity to link structural variation in these receptors to functional outcomes.

Here, we systematically characterize the WAK/WAKL gene family in P. vulgaris, integrating domain architecture, gene structure, phylogeny, synteny, and transcriptomic responses in resistant (Ouro Vermelho) versus susceptible (BRS Estilo) cultivars across infection time points. Using conserved domain annotation, PvWAKs and PvWAKLs were classified based on combinations of extracellular domains (EGF and GUB_WAK_bind) while retaining a conserved intracellular kinase core. Twenty-five distinct domains were identified, with specific sets being common or exclusive to each group, suggesting modular diversification of interaction interfaces. Phylogenetic and gene structure analyses revealed evolutionary patterns consistent with both conservation of signaling machinery and divergence in extracellular features. Integration with synteny supported retention of candidate orthologs across related species. RNA-Seq profiling at 0, 48, and 96 h post-inoculation uncovered complex, genotype- and time-dependent expression dynamics: subsets of PvWAK/WAKL genes were differentially expressed uniquely in resistant or susceptible backgrounds, while others displayed opposing temporal patterns, highlighting nuanced regulatory contributions to resistance. Combining structural and expression evidence yielded a prioritized list of PvWAK/WAKL candidates potentially underlying anthracnose resistance.

The study delineates how conserved kinase signaling is coupled to extracellular domain variability and dynamic expression to enable functional divergence within the WAK/WAKL family in P. vulgaris. The resulting candidate genes provide a focused basis for functional validation and may inform molecular breeding strategies for enhanced disease resistance.

The online version contains supplementary material available at 10.1186/s12864-026-12531-2.