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, 16(6), Article evae109. https://doi.org/10.1093/gbe/evae109
JYU authors or editors
Publication details
All authors or editors: Dittrich, 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 series: Genome Biology and Evolution
eISSN: 1759-6653
Publication year: 2024
Publication date: 16/05/2024
Volume: 16
Issue number: 6
Article number: evae109
Publisher: Oxford University Press
Publication country: United Kingdom
Publication language: English
DOI: https://doi.org/10.1093/gbe/evae109
Publication open access: Openly available
Publication channel open access: Open Access channel
Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/96190
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.
Keywords: amphibians; genome; transposons; sequencing; genomics; evolutionary biology; biodiversity
Free keywords: amphibians; genome evolution; transposable elements; long-reads; MobiSeq
Contributing organizations
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Ministry reporting: Yes
VIRTA submission year: 2024
Preliminary JUFO rating: 2