{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T01:02:57Z","timestamp":1773795777963,"version":"3.50.1"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T00:00:00Z","timestamp":1551830400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T00:00:00Z","timestamp":1551830400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish <jats:italic>Squalius alburnoides<\/jats:italic>. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of <jats:italic>S. alburnoides<\/jats:italic> and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in <jats:italic>S. alburnoides<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/s41598-019-40210-8","type":"journal-article","created":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T11:07:05Z","timestamp":1551870425000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Allele-specific expression variation at different ploidy levels in Squalius alburnoides"],"prefix":"10.1038","volume":"9","author":[{"given":"Isa","family":"Matos","sequence":"first","affiliation":[]},{"given":"Miguel P.","family":"Machado","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9882-5948","authenticated-orcid":false,"given":"Manfred","family":"Schartl","sequence":"additional","affiliation":[]},{"given":"Maria Manuela","family":"Coelho","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,3,6]]},"reference":[{"key":"40210_CR1","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1126\/science.1148910","volume":"318","author":"A Gimelbrant","year":"2007","unstructured":"Gimelbrant, A., Hutchinson, J. N., Thompson, B. R. & Chess, A. Widespread monoallelic expression on human autosomes. Science. 318, 1136\u201340, https:\/\/doi.org\/10.1126\/science.1148910 (2007).","journal-title":"Science."},{"key":"40210_CR2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-8-216","volume":"11","author":"M Prestel","year":"2010","unstructured":"Prestel, M., Feller, C. & Becker, P. B. Dosage compensation and the global re-balancing of aneuploid genomes. Genome Biology. 11, 216, https:\/\/doi.org\/10.1186\/gb-2010-11-8-216 (2010).","journal-title":"Genome Biology."},{"key":"40210_CR3","doi-asserted-by":"publisher","first-page":"R254","DOI":"10.1016\/j.cub.2011.02.035","volume":"21","author":"M Hegarty","year":"2011","unstructured":"Hegarty, M. Hybridization: expressing yourself in a crowd. Current Biology. 21, R254\u20135, https:\/\/doi.org\/10.1016\/j.cub.2011.02.035 (2011).","journal-title":"Current Biology."},{"key":"40210_CR4","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1101\/gr.102491.109","volume":"20","author":"CJ McManus","year":"2010","unstructured":"McManus, C. J. et al. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research. 20, 816\u2013825, https:\/\/doi.org\/10.1101\/gr.102491.109 (2010).","journal-title":"Genome Research."},{"key":"40210_CR5","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1093\/gbe\/evv057","volume":"7","author":"M-C Combes","year":"2015","unstructured":"Combes, M.-C. et al. Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids. Genome Biology and Evolution. 7, 1110\u20131121, https:\/\/doi.org\/10.1093\/gbe\/evv057 (2015).","journal-title":"Genome Biology and Evolution."},{"key":"40210_CR6","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.tig.2004.01.001","volume":"20","author":"JC Knight","year":"2004","unstructured":"Knight, J. C. Allele-specific gene expression uncovered. Trends in Genetics. 20, 113\u2013116, https:\/\/doi.org\/10.1016\/j.tig.2004.01.001 (2004).","journal-title":"Trends in Genetics."},{"key":"40210_CR7","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1146\/annurev.arplant.58.032806.103835","volume":"58","author":"ZJ Chen","year":"2007","unstructured":"Chen, Z. J. Genetic and Epigenetic Mechanisms for Gene Expression and Phenotypic Variation in Plant Polyploids. Annual Review of Plant Biology. 58, 377\u2013406, https:\/\/doi.org\/10.1146\/annurev.arplant.58.032806.103835 (2007).","journal-title":"Annual Review of Plant Biology."},{"key":"40210_CR8","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1111\/j.1469-8137.2012.04365.x","volume":"196","author":"CE Grover","year":"2012","unstructured":"Grover, C. E. et al. Homoeolog expression bias and expression level dominance in allopolyploids. New Phytologist. 196, 966\u2013971, https:\/\/doi.org\/10.1111\/j.1469-8137.2012.04365.x (2012).","journal-title":"New Phytologist."},{"key":"40210_CR9","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.1016\/0168-9525(96)81463-6","volume":"142","author":"M Guo","year":"1996","unstructured":"Guo, M., Davis, D. & Birchler, J. A. Dosage Effects on Gene Expression in a Maize Ploidy Series. 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