The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity
Year: 2025
Type: article
Abstract: Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we invoke the analogy of a kaleidoscope: while the DNA sequence represents its core, the genome has a dynamic, multidimensional configuration shaped by interactions across these features, generating an array of dimensions of genomic variation. In this perspective, we highlight underexplored dimensions of genomic variation that contribute to phenotypic diversity. We begin by revisiting the existence of noncanonical chromosomes and by emphasizing the role of large-scale structural changes and the 3D genome architecture in modulating genomic function. We then examine the regulatory mechanisms shaping transcriptional activity and genetic variation that, instead of regulating mean trait values, defines the degree of trait variability. Finally, we discuss the influence of sequence composition on its mutational potential. These dimensions, though rooted in sequence, are context dependent, interconnected, and often difficult to disentangle, reflecting a level of structural and regulatory complexity that challenges traditional genotype-phenotype models. By synthesizing recent findings across these dimensions, we argue for a broader framework for studying within-species genomic diversity: one that accounts for the diverse molecular architectures underlying phenotypic output. This expanded view not only deepens our knowledge of the genome itself but also contributes to our understanding of genome evolution and within-species phenotypic variation.
Source: Genome Biology and Evolution
DOI: 10.1093/gbe/evaf204
Institutions: SIB Swiss Institute of Bioinformatics, University of Lausanne, Princeton University, Universidad Nacional Autónoma de México, European Molecular Biology Laboratory, Max Planck Society, Friedrich Miescher Laboratory, University of Vienna, Universitat Autònoma de Barcelona, UNSW Sydney, TU Dortmund University, University of Copenhagen
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,850
Funders: National Science Foundation, Albert Ellis Institute, International Max Planck Research School for Environmental, Cellular and Molecular Microbiology, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Consejo Nacional de Ciencia y Tecnología, Institució Catalana de Recerca i Estudis Avançats, Max-Planck-Gesellschaft, Novo Nordisk, Ministerio de Ciencia e Innovación, Novo Nordisk Fonden, Ministerio de Asuntos Económicos y Transformación Digital, Gobierno de España, Australian Research Council, Agència de Gestió d'Ajuts Universitaris i de Recerca, Agencia Estatal de Investigación, HORIZON EUROPE Marie Sklodowska-Curie Actions
Awards: G1175115578, G1855990336, Methane Turnover in Alpine Glacier Forefields, G2262748287, G228714933, G2309174360, POPARCH: The role of POPulation scale genetic variation in chromosome 3D ARChitecture, G2855141111, G288263039, G3002584656, G300979063, Two to Tango: The synergistic power of RNA-protein interactions in plants, G3235642775, G3301491480, G3368120055, G3480869486, G3518538256, G3696983870, G425668148, G430777504, Selection on gene expression at different time scales and vertebrate Evo-Devo, G5080475149, G5421974903, G544591541, G5629889344, G5805502524, G5852091828, G6421209871, G7466406081, G8272058330, Modeling phenotypic and genomic changes across evolutionary scales, G8714223976, G8889690230, G8971761368, G99296377
OpenAlex ID: W4416192549