Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression.

Autor: An H; MU Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America., Pires JC; Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, United States of America., Conant GC; Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America.; Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America.; Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2024 Jan 16; Vol. 20 (1), pp. e1011803. Date of Electronic Publication: 2024 Jan 16 (Print Publication: 2024).
DOI: 10.1371/journal.pcbi.1011803
Abstrakt: Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 An et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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