Viruses and mobile genetic elements are significant components of plant genomes, comprising a large portion of their genetic material. These intragenomic elements suggest that virtually all organisms, across all kingdoms, are either infected with or densely populated by them, a phenomenon that has occurred since the beginning of life. A more detailed understanding of viral genomes reveals that most viral genes are found in animals, plants, or bacteria. After all, key aspects of gene physiology, genetic recombination, translation, transcription, and transposition, as conserved within the eukaryotic cell, were originally viral. In parallel, horizontal gene transfer is also widespread, producing tens or hundreds of active genes, and it appears to have contributed to the evolution of many, if not all, eukaryotes. New genetic combinations shaped by intragenomic elements and horizontal gene transfer provide the basis for innovative, adaptive modifications and developmental processes. However, despite these decisive genetic factors driving evolutionary innovation and species diversity, most studies have been monospecific, precluding drawing inter-specific trends from systematic compilation.

Therefore, this Research Topic seeks to offer a thorough examination of intragenomic elements derived from viral and bacterial origins within plant genomes, focusing on their evolution and adaptation consequences. By tackling how these elements alter plant genome dynamics, gene regulation, phenotypic diversity, and adaptation, we aim to unfold the complex network of genetic interactions and evolutionary strategies embedded in plant genomes.

To further our understanding in this topic, submissions should explore, but are not limited to the following themes:

• Mechanisms of Influence: Investigating how mobile genetic elements and other intragenomic elements regulate gene expression via insertional mutagenesis and epigenetic modifications

• Evolutionary Dynamics: Examining the evolutionary trajectories and interactions of intragenomic elements with plant genomes, especially in contexts involving whole-genome duplications and polyploidy

• Advances in Bioinformatics: Applying recent advances in machine learning and bioinformatics to generate new algorithms for identifying and classifying intragenomic elements in a variety of plant genomes

• Ecological and Agricultural Implications: Assessing how the dynamics of mobile intragenomic elements impact plant resilience and adaptability, particularly in agricultural settings to potentially enhance crop adaptation to environmental stresses

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Evolution and Adaptive Implications of Intragenomic Elements in Plant Genomes