A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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

JYU-tekijät tai -toimittajat

Julkaisun tiedot

Julkaisun kaikki tekijät tai toimittajat: 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.

Lehti tai sarja: Genome Biology and Evolution

eISSN: 1759-6653

Julkaisuvuosi: 2024

Ilmestymispäivä: 16.05.2024

Volyymi: Early online

Artikkelinumero: evae109

Kustantaja: Oxford University Press

Julkaisumaa: Britannia

Julkaisun kieli: englanti

DOI: https://doi.org/10.1093/gbe/evae109

Julkaisun avoin saatavuus: Avoimesti saatavilla

Julkaisukanavan avoin saatavuus: Kokonaan avoin julkaisukanava

Rinnakkaistallenteen verkko-osoite (pre-print): https://doi.org/10.1101/2023.11.06.565769

Tiivistelmä

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.

YSO-asiasanat: sammakkoeläimet; perimä; transposonit; sekvensointi; genomiikka; evoluutiobiologia; biodiversiteetti

Vapaat asiasanat: amphibians; genome evolution; transposable elements; long-reads; MobiSeq

Liittyvät organisaatiot

Hankkeet, joissa julkaisu on tehty

OKM-raportointi: Kyllä

Raportointivuosi: 2024

Alustava JUFO-taso: 2