Genome size evolution and phenotypic correlates in the poison frog family Dendrobatidae DOI Creative Commons
Tyler E. Douglas, Roberto Márquez, V Renee Holmes

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 2, 2023

Abstract Adaptive and neutral processes have produced a spectrum of genome sizes across organisms. Amphibians in particular possess wide range C-values, from <1 pg to over 125 pg. However, the size most amphibians is unknown, no single family has been comprehensively assessed. We provide new estimates for 32 poison frog species representing major lineages within Dendrobatidae using Feulgen staining museum specimens flow cytometry fresh tissue. show that likely evolves under an Ornstein–Uhlenbeck process, potentially with evolutionary rate shifts genera Phyllobates Hyloxalus , which respectively largest (13.0 pg) second smallest (2.6 genomes family. Phylogenetically controlled analyses indicate positively correlated snout-vent-length, oocyte number, clutch size, but negatively active metabolic scope. While body are also correlates toxicity, we found relationship between evolution chemical defense Dendrobatidae. Our assessment provides insight into shaping short timescales dataset will facilitate investigations mechanistic links organismal physiology. Resumen Los procesos adaptativos y neutrales han producido un espectro de tamaños genoma en los organismos. anfibios poseen una amplia gama valores C, desde hasta más Sin embargo, se desconoce el tamaño del la mayoría ha evaluado exhaustivamente ninguna familia. Proporcionamos nuevas estimaciones para especies ranas venenosas que representan principales linajes dentro utilizando tinción con especímenes museo citometría flujo tejido fresco. Mostramos probablemente evolucione bajo proceso Ornstein-Uhlenbeck, potencialmente cambios tasa evolutiva géneros e respectivamente grande (13,0 segundo pequeño (2,6 análisis filogenéticamente controlados indican correlaciona positivamente longitud hocico-cloaca, número ovocitos nidada, pero negativamente metabólica activa alcance metabólico. Aunque corporal correlacionan toxicidad, encontramos relación entre evolución defensa química Nuestra evaluación proporciona información sobre dirigen escalas tiempo cortas conjunto datos facilitará las investigaciones vínculos mecánicos fisiología organismo.

Language: Английский

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides DOI Creative Commons
Simon Tang, Emma Peel, Katherine Belov

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Feb. 18, 2024

Abstract The number of genome-level resources for non-model species continues to rapidly expand. However, frog remain underrepresented, with up 90% genera having no genomic or transcriptomic data. Here, we assemble the first and recently described southern stuttering ( Mixophyes australis ). is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing Hi-C scaffolding, generated a high-quality genome assembly, scaffold N50 369.3 Mb 95.1% contained twelve scaffolds. this identified mitochondrial genome, assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences two families antimicrobial peptides (AMPs) frog, cathelicidins β-defensins. While traditional peptidomic approaches peptide discovery have typically one AMPs from skin secretions, our bioinformatic approach discovered 12 β-defensins that were expressed range tissues. investigated novelty found diverse predicted activities. Our highlights benefits multi-omics contributes valuable an under-represented taxon.

Language: Английский

Citations

3
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation DOI Creative Commons
Tiffany A. Kosch, María Torres‐Sánchez, H. Christoph Liedtke

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 1, 2024

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding features this animal class that other terrestrial vertebrates. The need for genomic resources is more urgent than ever due to increasing threats group. are one most imperiled taxonomic groups, with approximately 41% species threatened extinction habitat loss, changes in land use patterns, disease, climate change, synergistic effects. Amphibian have provided better ontogenetic diversity, tissue regeneration, life history reproductive modes, antipredator strategies, resilience adaptive responses. They also serve as essential models studying broad traits, such evolutionary genome expansions contractions, they exhibit widest range sizes among all taxa possess multiple mechanisms genetic sex determination. Despite these features, sequencing amphibians has significantly lagged behind vertebrates, primarily challenges assembling large, repeat-rich genomes relative lack societal support. emergence long-read technologies, combined advanced molecular computational techniques improve scaffolding reduce workloads, now making it possible address some challenges. To promote accelerate production research international coordination collaboration, we launched Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) early 2023. This burgeoning community already 282 members from 41 countries. AGC aims leverage capabilities its advance bridge implementation gap biologists, bioinformaticians, conservation practitioners. Here evaluate state field genomics, highlight previous studies, present overcome, call on communities unite part enable "leap" next level.

Language: Английский

Citations

3
Comparative transcriptomics reveals that a novel form of phenotypic plasticity evolved via lineage‐specific changes in gene expression DOI Creative Commons
Andrew J. Isdaner, Nicholas A. Levis, David W. Pfennig

et al.

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(10)

Published: Oct. 1, 2023

Novel forms of phenotypic plasticity may evolve by lineage-specific changes or co-opting mechanisms from more general plasticity. Here, we evaluated whether a novel resource polyphenism in New World spadefoot toads (genus

Language: Английский

Citations

5
Genome size evolution and phenotypic correlates in the poison frog family Dendrobatidae DOI Creative Commons
Tyler E. Douglas, Roberto Márquez, V Renee Holmes

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 2, 2023

Abstract Adaptive and neutral processes have produced a spectrum of genome sizes across organisms. Amphibians in particular possess wide range C-values, from <1 pg to over 125 pg. However, the size most amphibians is unknown, no single family has been comprehensively assessed. We provide new estimates for 32 poison frog species representing major lineages within Dendrobatidae using Feulgen staining museum specimens flow cytometry fresh tissue. show that likely evolves under an Ornstein–Uhlenbeck process, potentially with evolutionary rate shifts genera Phyllobates Hyloxalus , which respectively largest (13.0 pg) second smallest (2.6 genomes family. Phylogenetically controlled analyses indicate positively correlated snout-vent-length, oocyte number, clutch size, but negatively active metabolic scope. While body are also correlates toxicity, we found relationship between evolution chemical defense Dendrobatidae. Our assessment provides insight into shaping short timescales dataset will facilitate investigations mechanistic links organismal physiology. Resumen Los procesos adaptativos y neutrales han producido un espectro de tamaños genoma en los organismos. anfibios poseen una amplia gama valores C, desde hasta más Sin embargo, se desconoce el tamaño del la mayoría ha evaluado exhaustivamente ninguna familia. Proporcionamos nuevas estimaciones para especies ranas venenosas que representan principales linajes dentro utilizando tinción con especímenes museo citometría flujo tejido fresco. Mostramos probablemente evolucione bajo proceso Ornstein-Uhlenbeck, potencialmente cambios tasa evolutiva géneros e respectivamente grande (13,0 segundo pequeño (2,6 análisis filogenéticamente controlados indican correlaciona positivamente longitud hocico-cloaca, número ovocitos nidada, pero negativamente metabólica activa alcance metabólico. Aunque corporal correlacionan toxicidad, encontramos relación entre evolución defensa química Nuestra evaluación proporciona información sobre dirigen escalas tiempo cortas conjunto datos facilitará las investigaciones vínculos mecánicos fisiología organismo.

Language: Английский

Citations

1