image: Sankey diagram illustrating the inferred functions of TE-proximal genes. The width of connections between each vertical block represents the gene count, delineating GO term classifications associated with TE-proximal genes, the number of genes adjacent to three distinct types of TEs, genes categorized across nine species, and the GO term classifications of TE-proximal genes. TE-proximal gene GO terms are categorized into five primary groups: morphogenesis, substance binding, enzyme activity, metabolism, and others. Each group encompasses various detailed GO term descriptions representing specific gene functions.
Credit: Horticulture Research
Transposable elements (TEs) significantly impact plant genome structure and function. This study examines the distribution, activity, and expression patterns of TEs across 14 Rosaceae species. The findings reveal distinct evolutionary patterns of long terminal repeat retrotransposons (LTR-RTs) and their influence on genes linked to adversity resistance, morphogenesis, enzyme activity, and metabolic processes. These insights advance our understanding of Rosaceae genome evolution and gene regulation.
Transposable elements are mobile DNA sequences that play a crucial role in plant genome architecture and gene regulation. They drive genome size variation and affect gene expression by altering regulatory networks. Despite their significance, the diverse and dynamic roles of Transposable elements (TEs) are not well understood. To address these complexities, in-depth studies are necessary to explore Transposable element (TE) activity, distribution, and their effects on gene regulation. This research focuses on the Rosaceae family, aiming to uncover the impact of TEs on genome evolution and functional diversity.
Conducted by a team from Northwest A&F University, this research (DOI: 10.1093/hr/uhae118) was published on April 26, 2024, in Horticulture Research. The study investigates transposable elements in 14 Rosaceae genomes, examining their distribution, transposition activity, expression patterns, and influence on differentially expressed genes. The goal is to provide comprehensive insights into how TEs shape genome evolution and gene regulation in Rosaceae.
The study analyzed 14 representative Rosaceae genomes, revealing distinct evolutionary patterns of long terminal repeat retrotransposons (LTR-RTs) and their effects on genome size and gene expression. Genes near recent TE insertions were associated with adversity resistance, while those near older insertions were linked to morphogenesis, enzyme activity, and metabolic processes. The research highlights diverse responses of LTR-RTs to various conditions, demonstrating their significant role in plant genome evolution. Additionally, 3695 pairs of syntenic differentially expressed genes (DEGs) near TEs in apple varieties were identified, suggesting that TE insertions contribute to varietal trait differences. This analysis provides new insights into the role of TEs in shaping the genomic landscape and regulatory mechanisms within the Rosaceae family.
Dr. Yaqiang Sun, one of the corresponding authors, stated, "Our findings underscore the pivotal role of transposable elements in shaping the genomic architecture and functional diversity within the Rosaceae family. This research provides a valuable resource for future studies on genome evolution and the regulatory mechanisms of TEs."
The insights from this study have significant implications for plant breeding and genetic engineering. Understanding the role of TEs in gene regulation and genome evolution can help develop new strategies for crop improvement, particularly in enhancing stress resistance and optimizing desirable traits in Rosaceae species. This research also sets the stage for further exploration of TEs in other plant families, contributing to a broader understanding of plant genome dynamics.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae118
Funding information
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.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
Journal
Horticulture Research
Subject of Research
Not applicable
Article Title
Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation
Article Publication Date
26-Apr-2024
COI Statement
The authors declare that they have no competing interests.