Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation

Abstract

Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. ‘Gala’ and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (32102338) and the Chinese Universities Scientific Fund (2452021133 and 2452023067). The authors thank High-Performance Computing (HPC) of Northwest A&F University (NWAFU) for providing computing resources.

Author contributions

T.Z., F.M., Y.Z., and Y.S. designed the study. Z.Y., J.L., H.W., X.L., B.P., Z.L., and B.G. conducted the analyses. Z.Y., Q.Y., and B.G. analyzed the data. Z.Y. and T.Z. wrote the paper. All co-authors read and edited the manuscript.

Data availability

Data sets used in this study are available as online supplementary material.

Conflicts of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data are available at Horticulture Research online.

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