# A pangenome insight into the genome divergence and flower color diversity among Rhododendron species

## TL;DR

This study explores how transposable elements influence genome divergence and flower color diversity in Rhododendron species.

## Contribution

The study provides new insights into the role of transposable elements in driving genomic and flower color diversity in Rhododendron.

## Key findings

- Approximately 50% of Rhododendron genomes consist of transposable elements, with over half being LTR-RTs.
- Transposable elements are significantly associated with genomic differentiation and structural variances.
- Gene duplication and loss related to flower color may be driven by transposable elements.

## Abstract

The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.

Here, we collected whole-genome data from seven rhododendrons of different subgenera to investigate the patterns of interspecific genomic and sequence divergence, as well as evolutionary dynamics of gene family related to flower color. We discovered that approximately 50% of Rhododendron genomes are composed of transposable elements (TEs), with over half of them being long terminal repeat retrotransposons (LTR-RTs). TEs significantly associate with genomic differentiation and structural variances within the genus. Additionally, the duplication and loss of genes associated with flower color and their corresponding expression over time are potentially driven by TEs.

Our comparative genomic analysis accentuates the critical role of TEs in genome divergence within the Rhododendron genus, highlighting their potential role as a key factor governing speciation and interspecific variability within the genus.

The online version contains supplementary material available at 10.1186/s12864-025-12461-5.