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dc.contributor.authorDittrich, Carolin
dc.contributor.authorHoelzl, Franz
dc.contributor.authorSmith, Steve
dc.contributor.authorFouilloux, Chloe A.
dc.contributor.authorParker, Darren J.
dc.contributor.authorO’Connell, Lauren A.
dc.contributor.authorKnowles, Lucy S.
dc.contributor.authorHughes, Margaret
dc.contributor.authorFewings, Ade
dc.contributor.authorMorgan, Rhys
dc.contributor.authorRojas, Bibiana
dc.contributor.authorComeault, Aaron A.
dc.date.accessioned2024-06-27T11:52:37Z
dc.date.available2024-06-27T11:52:37Z
dc.date.issued2024
dc.identifier.citationDittrich, C., Hoelzl, F., Smith, S., Fouilloux, C. A., Parker, D. J., O’Connell, L. A., Knowles, L. S., Hughes, M., Fewings, A., Morgan, R., Rojas, B., & Comeault, A. A. (2024). Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution. <i>Genome Biology and Evolution</i>, <i>16</i>(6), Article evae109. <a href="https://doi.org/10.1093/gbe/evae109" target="_blank">https://doi.org/10.1093/gbe/evae109</a>
dc.identifier.otherCONVID_213720805
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/96190
dc.description.abstractGenome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimise primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.en
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherOxford University Press
dc.relation.ispartofseriesGenome Biology and Evolution
dc.rightsCC BY-NC 4.0
dc.subject.otheramphibians
dc.subject.othergenome evolution
dc.subject.othertransposable elements
dc.subject.otherlong-reads
dc.subject.otherMobiSeq
dc.titleGenome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-202406275032
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.type.coarhttp://purl.org/coar/resource_type/c_2df8fbb1
dc.description.reviewstatuspeerReviewed
dc.relation.issn1759-6653
dc.relation.numberinseries6
dc.relation.volume16
dc.type.versionpublishedVersion
dc.rights.copyright© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution
dc.rights.accesslevelopenAccessfi
dc.relation.grantnumber319949
dc.relation.grantnumber318404
dc.relation.grantnumber345974
dc.subject.ysobiodiversiteetti
dc.subject.ysogenomiikka
dc.subject.ysoperimä
dc.subject.ysotransposonit
dc.subject.ysosammakkoeläimet
dc.subject.ysosekvensointi
dc.subject.ysoevoluutiobiologia
dc.format.contentfulltext
jyx.subject.urihttp://www.yso.fi/onto/yso/p5496
jyx.subject.urihttp://www.yso.fi/onto/yso/p5146
jyx.subject.urihttp://www.yso.fi/onto/yso/p8862
jyx.subject.urihttp://www.yso.fi/onto/yso/p27134
jyx.subject.urihttp://www.yso.fi/onto/yso/p16762
jyx.subject.urihttp://www.yso.fi/onto/yso/p25917
jyx.subject.urihttp://www.yso.fi/onto/yso/p21944
dc.rights.urlhttps://creativecommons.org/licenses/by-nc/4.0/
dc.relation.doi10.1093/gbe/evae109
dc.relation.funderResearch Council of Finlanden
dc.relation.funderResearch Council of Finlanden
dc.relation.funderResearch Council of Finlanden
dc.relation.funderSuomen Akatemiafi
dc.relation.funderSuomen Akatemiafi
dc.relation.funderSuomen Akatemiafi
jyx.fundingprogramResearch costs of Academy Research Fellow, AoFen
jyx.fundingprogramAcademy Research Fellow, AoFen
jyx.fundingprogramResearch costs of Academy Research Fellow, AoFen
jyx.fundingprogramAkatemiatutkijan tutkimuskulut, SAfi
jyx.fundingprogramAkatemiatutkija, SAfi
jyx.fundingprogramAkatemiatutkijan tutkimuskulut, SAfi
jyx.fundinginformationThis work was supported by funding from the NERC Environmental Omics Facility (project number 1382 to AAC); Research Council of Finland (# 318404; 319949; 345974 to BR); and the National Science Foundation (IOS-1822025 and IOS-1827333 to LAO).
dc.type.okmA1


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