The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

Myers, Edward A; Pyron, R. Alexander

doi:10.1101/2024.04.30.591895

Cited by 2 publications

(1 citation statement)

References 53 publications

(137 reference statements)

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“…There are considerably fewer reference genomes for amphibians than exist for birds (N=754), mammals (N=406), and non-avian reptiles (N=108). This scarcity of reference genomes results in many gaps in genome representation across the amphibian tree of life including many entirely unrepresented groups and with only two genomes representing the entire order Caudata (but see Myers & Pyron, 2024). The unrepresented families include many of interest from a conservation perspective due to their high number of IUCN RedList Critically Endangered species (e.g., Cryptobranchidae, Plethodontidae, Strabomantidae, and Craugastoridae) (IUCN, 2022).…”

Section: Discussionmentioning

confidence: 99%

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

Kosch

Crawford

Mueller

et al. 2023

Preprint

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Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They have many unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination, and in some lineages even the ability to regenerate limbs and internal organs. Although genomics approaches would shed light on these unique phenotypic traits and aid in conservation management, the sequencing and assembly of amphibian genomes has lagged far behind other taxa due to their comparatively large genome size. Fortunately, the development of long-read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes, and lack of high-quality assemblies in multiple clades of amphibians. Here we analyze 32 publicly available amphibian genomes to evaluate their usefulness for functional genomics analysis. We report considerable variation in assembly quality and completeness, and report some of the highest repeat content of any vertebrate. We also provide evidence of conservation of genome synteny despite the long divergence times of this group but show that chromosome naming and orientation has been inconsistent across genome assemblies. Additionally, we discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Lastly, we propose increased investment in amphibian genomics research to promote their conservation.

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Section: Discussionmentioning

confidence: 99%

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

Kosch

Crawford

Mueller

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

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

Kosch,

Crawford,

Lockridge Mueller

et al. 2024

Molecular Ecology Resources

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

show abstract

The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

Cited by 2 publications

References 53 publications

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

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

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

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