DNA transposon expansion is associated with genome size increase in mudminnows

• Published in: Genome Biology and Evolution
• Main Authors: Lehmann, Robert, Kovařík, Aleš, Ocalewicz, Konrad, Kirtiklis, Lech, Zuccolo, Andrea, Tegner, Jesper, Wanzenböck, Josef, Bernatchez, Louis, Lamatsch, Dunja K, Symonová, Radka
• Other Authors: Biological and Environmental Science and Engineering (BESE) Division, Laboratory of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Science, Královopolská 135, Brno, 61265, Czech Republic, Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Gdansk, Poland, Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, M. Oczapowskiego Str. 5, 10-718, Olsztyn, Poland, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, 56127, Italy, Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, A—5310, Austria, IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada, Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany, Faculty of Biology, University of Hradec Kralove, Czech Republic
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Oxford University Press (OUP) 2021
• Subjects: Guillaume; Alaska blackfish; Dallia pectoralis; Alaska
• Online Access: http://hdl.handle.net/10754/672064; https://doi.org/10.1093/gbe/evab228

Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5-5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in Umbra limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage. This study was supported by the Tyrolean funds project with contract Nr. UNI-0404/2015 to RS. The authors are also grateful to the`Excelence projekt PřF UHK 2209/2018` and the Czech Science Foundation (19-03442S) for financial support. RS acknowledges the EuroTech Postdoc Programmewhich is co-funded by the European Commission under its framework programme Horizon 2020, Grant Agreement number 754462. We acknowledge Petr Ráb for discussion on genome size in the Umbra genus, Guillaume Côté for fishing Umbra and Esox in Québec, and we also acknowledge Maria Pichler of UIBK for her technical support.