A1 Journal article (refereed)
Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution (2024)


Dittrich, 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. Genome Biology and Evolution, Early online, Article evae109. https://doi.org/10.1093/gbe/evae109


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Publication details

All authors or editorsDittrich, Carolin; Hoelzl, Franz; Smith, Steve; Fouilloux, Chloe A.; Parker, Darren J.; O’Connell, Lauren A.; Knowles, Lucy S.; Hughes, Margaret; Fewings, Ade; Morgan, Rhys; et al.

Journal or seriesGenome Biology and Evolution

eISSN1759-6653

Publication year2024

Publication date16/05/2024

VolumeEarly online

Article numberevae109

PublisherOxford University Press

Publication countryUnited Kingdom

Publication languageEnglish

DOIhttps://doi.org/10.1093/gbe/evae109

Publication open accessOpenly available

Publication channel open accessOpen Access channel

Web address of parallel published publication (pre-print)https://doi.org/10.1101/2023.11.06.565769


Abstract

Genome 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.


Keywordsamphibiansgenometransposonssequencinggenomicsevolutionary biologybiodiversity

Free keywordsamphibians; genome evolution; transposable elements; long-reads; MobiSeq


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Last updated on 2024-24-05 at 07:19