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.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 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, anti-predator 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

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration DOI Creative Commons
Tom Brown, Ketan Mishra, Ahmed Elewa

et al.

Cell Genomics, Journal Year: 2025, Volume and Issue: unknown, P. 100761 - 100761

Published: Jan. 1, 2025

Language: Английский

Citations

1
A chromosome-level genome assembly of the European green toad (Bufotes viridis) DOI Creative Commons
Patrik Rödin‐Mörch, Ignas Bunikis,

Eunkyoung Choi

et al.

G3 Genes Genomes Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

Abstract The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status labeled as of least concern by IUCN, it declining in many parts its range where populations are fragmented and isolated. A high-quality reference genome an important resource for genomic researchers who trying to understand interpret signals population decline, inbreeding, accumulation deleterious mutations. Here, we assembled annotated a chromosome-level B. viridis part Reference Genome Atlas pilot project. assembly, with size ∼3.89 Gb consists 11 chromosomes additional 2,096 unplaced scaffolds. final assembly had scaffold N50 value 478.39 Mb covered 90.4% single copy tetrapod orthologs, 46.7% repetitive elements. Finally, total 23,830 protein-coding genes matching known gene, together 56,974 mRNAs were predicted. This will benefit amphibian evolutionary genomics research enable genetic studies inform practical work on this species.

Language: Английский

Citations

0
A phylogenetic analysis of the CDKL protein family unravels its evolutionary history and supports the Drosophila model of CDKL5 deficiency disorder DOI Creative Commons

María del Carmen Martín-Carrascosa,

Christian Palacios-Martínez,

Máximo Ibo Galindo

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2025, Volume and Issue: 13

Published: April 30, 2025

The human CDK-like (CDKL) family of serine‒threonine kinases has five members (CDKL1-5), with a conserved N-terminal kinase domain and variable C-termini. Among these, CDKL5 is particular interest because its involvement in deficiency disorder (CDD), rare epileptic encephalopathy several comorbidities for which there are no specific treatments. Current CDD vertebrate models seizure resistant, could be explained by the genetic background, including leaky expression other CDKLs. Thus, phylogenetic analysis protein would valuable understanding current developing new ones. Our studies revealed that ancestral CDKLs were present all major eukaryotic clades had ciliary/flagellar functions, may have diversified throughout evolution. original CDKL, was likely similar to CDKL5, gave rise remaining through successive duplications. In addition, undergone further gene duplication loss, pattern suggests some functional redundancy among them. A separate study focusing on C-terminal tail suggested this only functionally relevant jawed vertebrates. We developed model Drosophila based downregulation single Cdkl RNAi, results phenotypes those patients, rescued re-expression fly . CDKL proteins contain domain, originally involved ciliary maintenance; therefore, invertebrate organisms can used investigate functions involve aforementioned domain.

Language: Английский

Citations

0
Large tandem repeats of grass frog (Rana temporaria) in silico and in situ DOI Creative Commons
M. Popova, Aleksey Komissarov, Д. И. Остромышенский

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 6, 2025

Genomes of higher eukaryotes contain a large fraction non-coding repetitive DNA, including tandem repeats (TRs) and transposable elements (TEs). The impact TRs on genome structure function the importance TR transcripts have been described for several model species. Amphibians one most diverse sizes among vertebrates, attributed to abundance DNA. Consequently, amphibians are good models analysis sequences, TRs. However, few studies focused amphibian genomes. Bioinformatic analyses were performed characterise content localisation in sequenced grass frog Rana temporaria genome. By applying different bioinformatic approaches, 76 families 314 single arrays (not grouped into families) identified. Each was characterised basis chromosomal position, monomer length variability GC content. revealed great diversity TRs, with clear predominance short monomers (< 100 bp), although long (> 1000 bp) also exist. six abundant successfully mapped by fluorescence situ hybridization (FISH), which highlighted presence specific sequences strategic regions, i.e., pericentromeric regions. A comparison results silico mapping some inaccuracies assembly heterochromatic putative new non-autonomous TE called "FEDoR" (Frog Element Dispersed organised Repeat) is described. FEDoR ∼ 3.5 kb length, has no significant similarity any known family, contains multiple internal motifs, flanked both sides pairs inverted repeat (IRSs) target site duplications (TSDs). Characterisation this species provided insights regarding biology Anuran amphibians.

Language: Английский

Citations

0
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
The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione) DOI Creative Commons
Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov

et al.

F1000Research, Journal Year: 2023, Volume and Issue: 12, P. 845 - 845

Published: July 18, 2023

The Kroombit tinkerfrog (

Language: Английский

Citations

6
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.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 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, anti-predator 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

1