# Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics

## TL;DR

This study uses comparative genomics to identify conserved gene regulatory elements in common bean, offering insights for crop improvement.

## Contribution

A validated comparative genomics method to predict conserved transcription factor binding sites in Phaseolus vulgaris.

## Key findings

- Identified TFBS for 12,631 bean genes with an average of 6 conserved motifs per gene.
- ERF, MYB, and bHLH transcription factor families were most prevalent in conserved motifs.
- A significant link was found between motif count and experimental evidence of gene regulation.

## Abstract

Common bean (Phaseolus vulgaris), a staple food in Latin America and Africa, serves as a vital source of energy, protein, and essential minerals for millions of people. However, genomics knowledge that breeders could leverage for improvement of this crop is scarce. We have developed and validated a comparative genomics approach to predict conserved transcription factor binding sites (TFBS) in common bean and studied gene regulatory networks. We analyzed promoter regions and identified TFBS for 12,631 bean genes with an average of 6 conserved motifs per gene. Moreover, we discovered a statistically significant relationship between the number of conserved motifs and amount of available experimental evidence of gene regulation. Notably, ERF, MYB, and bHLH transcription factor families dominated conserved motifs, with implications for starch biosynthesis regulation. Furthermore, we provide gene regulatory data as a resource that can be interrogated for the regulatory landscape of any set of genes. Our results underscore the significance of TFBS conservation in legumes and aligns with the notion that core genes often exhibit a more conserved regulatory makeup. The study demonstrates the effectiveness of a comparative genomics approach for addressing genome information gaps in non-model organisms and provides valuable insights into the regulatory networks governing starch biosynthesis genes that can support crop improvement programs.

The online version contains supplementary material available at 10.1186/s12864-025-11309-2.