Comparative analysis of amphibian genomes: An emerging resource for basic and applied research

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 4, 2024

Abstract Amphibians are the most threatened group of vertebrates and in dire need conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity reproductive strategies, permeable specialized skin capable producing toxins antimicrobial compounds, multiple genetic mechanisms sex determination some lineages, ability regenerate limbs organs. Although genomic approaches would shed light on these traits aid conservation, sequencing assembly amphibian genomes has lagged behind other taxa due comparatively large genome sizes. Fortunately, development long‐read technologies initiatives led recent burst new assemblies. growing, field genomics suffers from lack annotation resources, tools for working with challenging high‐quality assemblies clades amphibians. Here, we analyse 51 publicly available evaluate usefulness functional research. We report considerable variation quality completeness highest transposable element repeat contents any vertebrate. Additionally, detected an association between content climatic variables. Our analysis provides evidence conserved synteny despite long divergence times this group, but also highlight inconsistencies chromosome naming orientation across discuss gaps phylogeny suggest key targets future endeavours. Finally, propose increased investment research promote conservation.

Language: Английский

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A chromosome-level genome assembly of the European green toad (Bufotes viridis)

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

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A Chromosome-level genome assembly of the American bullfrog (Aquarana catesbeiana)

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: March 10, 2025

The American bullfrog (Aquarana catesbeiana) is both an economically important aquaculture species and a globally distributed invasive organism with high environmental adaptability. In this study, we present high-quality chromosome-level genome assembly for the species, comprising 13 chromosomes total length of 6.32 Gb scaffold N50 691.8 Mb. Genome completeness was evaluated at 95.5% using BUSCO 99.9% Merqury. Repetitive sequences accounted 79.51% genome. Through combination RNA-seq, Ab initio homology-based gene prediction, identified 32,382 protein-coding genes, 98.96% these genes functionally annotated. This provides resource future studies on evolution, functional genomics molecular breeding bullfrog.

Language: Английский

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Karyotype and genome size analyses for two spiders of the lycosidae family

Frontiers in Genetics, Journal Year: 2025, Volume and Issue: 16

Published: March 25, 2025

Background Karyotype and genome size are critical genetic characteristics with significant value for cytogenetics, taxonomy, phylogenetics, evolution, molecular biology. The Lycosidae family, known its diverse spiders varying ecological habits behavioral traits, has seen limited exploration of karyotype size. Methods We utilized an improved tissue drop technique to prepare chromosome slides compare the features male female karyotypes two wolf different Lycosidae. Furthermore, we predicted their sizes using flow cytometry (FCM) K-mer analysis. Results Hippasa lycosina were 2n♀ = 26 14 m + 12 sm 2n♂ 24 10 sm, respectively, composed metacentric (m) submetacentric (sm) chromosomes. In contrast, Lycosa grahami consisted telocentric (t) subtelocentric (st) chromosomes (2n♀ 20 20th 18 12th 6t, females males). sex both X 1 2 O. estimated H. L. genomes 1966.54–2099.89 Mb 3692.81–4012.56 Mb, respectively. Flow yielded slightly smaller estimates compared k-mer analysis revealed a heterozygosity 0.42% 0.80% , along duplication ratios 21.39% 54.91%, Conclusion This study describes first from that exhibit differential provides essential data future phylogenetic, cytogenetic, genomic studies.

Language: Английский

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Large tandem repeats of grass frog (Rana temporaria) in silico and in situ

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

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The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

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

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Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(6)

Published: May 15, 2024

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display greatest variation in genome size, making them ideal models explore causes consequences However, high-quality assemblies for have, until recently, been rare. Here, we generate a assembly dyeing poison frog, Dendrobates tinctorius. We compare publicly available frog genomes find evidence both large-scale conserved synteny widespread rearrangements between lineages. Comparing orthologs annotated these revealed strong correlation gene size. To cause gene-size variation, quantified location relative features that accumulation introns has played role evolution D. tinctorius, while estimates insertion times suggest many events recent species-specific. Finally, carry out population-scale mobile-element sequencing show diversity abundance can complicate genotyping from repetitive element sequence anchors. Our results have clearly large Future studies needed fully understand dynamics optimize primer or bait design cost-effective population-level species with large, genomes.

Language: Английский

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Comparative analysis of amphibian genomes: an emerging resource for basic and applied research

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

Published: March 1, 2023

ABSTRACT Amphibians are the most threatened group of vertebrates and in dire need conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity reproductive strategies, permeable specialized skin capable producing toxins antimicrobial compounds, multiple genetic mechanisms sex determination, some lineages, ability regenerate limbs organs. Although genomics approaches would shed light on these traits aid conservation, sequencing assembly amphibian genomes has lagged behind other taxa due comparatively large genome sizes. Fortunately, development long-read technologies initiatives led recent burst new assemblies. growing, field suffers from lack annotation resources, tools for working with challenging genomes, high-quality assemblies clades amphibians. Here we analyze 51 publicly available evaluate usefulness functional research. We report considerable variation quality completeness, highest transposable element repeat contents any vertebrate. Additionally, detected an association between content climatic variables. Our analysis provides evidence conserved synteny despite long divergence times this group, but also highlight inconsistencies chromosome naming orientation across discuss gaps phylogeny suggest key targets future endeavors. Finally, propose increased investment research promote conservation.

Language: Английский

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Repeat-rich regions cause false positive detection of NUMTs - a case study in amphibians using an improved cane toad reference genome

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

Published: July 6, 2024

Abstract Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear of mitochondrial origin (NUMT) can confound studies phylogenetic relationships and mtDNA heteroplasmy. Homology searches with are to detect NUMTs the genome. Nevertheless, false positive detection is common when handling repeat-rich sequences, whilst fragmented genomes might result missing true NUMTs. In this study, we investigated different NUMT methods how quality genome assembly affects them. We presented an improved (aRhiMar1.3) invasive cane toad ( Rhinella marina ) additional long-read Nanopore 10x linked-read sequencing. The final was 3.47 Gb length 91.3% tetrapod universal single-copy orthologs (n=5,310), indicating gene-containing regions were well assembled. three complementary (NUMTFinder, dinumt PALMER study landscape All yielded consistent results, showing very few Furthermore, expanded analyses other amphibians confirmed a weak relationship between size number present Amphibians repeat-rich, show that found highly repetitive prone inflation using homology-based without filters. Together, provides exemplar robustly identify complex confounding effects on concern. Significance This uses updated multiple confirm lack use as population genetic marker toad. provide accounting composition, highlight risks BLASTN-based approaches genomes.

Language: Английский

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The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

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

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