A genomic perspective on the origins, evolution and adaptation of Galápagos iguanas

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

Abstract Island systems provide unique opportunities to explore the genomic basis of species diversification and novel trait evolution driven by adaptation environmental challenges exploitation new ecological niches. Here we generate first sequences for four Galápagos iguana show that they evolved in situ into marine Amblyrhynchus land Conolophus sister lineages on now submerged islands, following a single colonisation event approximately 13 million years ago, with evidence recent inbreeding coincident timing human settlement. Selection scans identified genes linked traits facilitating adaption environment, including specialised pigmentation phenotypes, as well DNA damage UV irradiation inflammation responses. These may contribute adaptive enhanced cancer resistance, relation elevated exposure at equatorial latitudes. In iguana, under positive selection are associated their transition underwater foraging, ability repeatedly shrink grow body size. Our study provides insights origins iguanas molecular life Galápagos, future conservation management threatened iguanid populations.

Language: Английский

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New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: Dec. 8, 2023

Abstract Background Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain conspicuous gap in molecular studies of marine adaptation vertebrates. Results Here, we generate four new annotated snake genomes, three these at chromosome-scale ( Hydrophis major , H . ornatus and H. curtus ), perform detailed comparative genomic analyses their closest terrestrial relatives. Phylogenomic highlight possibility near-simultaneous speciation root synteny maps show intra-chromosomal variations that will be important targets for future this system. We then used strict screen positive selection (against background seven genomes) identify genes over-represented hypoxia adaptation, sensory perception, immune response morphological development. Conclusions provide best reference genomes currently available prolific medically elapid radiation. Our phylogenetic complexity conserved genome structure Positively selected marine-associated promising candidates future, functional linking genetic signatures phenotypes other

Language: Английский

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Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics

Journal of Heredity, Journal Year: 2024, Volume and Issue: 115(5), P. 487 - 497

Published: May 9, 2024

We present genome assemblies for 18 snake species representing families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new assemblies, we extracted thousands of loci commonly used in systematic phylogenomic studies on snakes, including target-capture datasets composed ultraconserved elements (UCEs) anchored hybrid enriched (AHEs), as well traditional Sanger loci. Phylogenies inferred from the two were identical with each other strongly congruent previously published phylogenies. To show additional utility non-model genomes investigative evolutionary research, mined New Guinea island endemics our dataset (S. admiraltiensis T. doriae) ATP1a3 gene, a thoroughly researched indicator resistance to toad toxin ingestion by squamates. find that both snakes possess genotype despite their endemism Guinea, region absent any toads until human-mediated introduction Cane Toads 1930s. These substitutions suggest same bufotoxin Australian congenerics (Stegonotus australis mairii) which forage invasive Toads. Herein, short-read high-coverage genomes, improving deficit available squamate associated voucher specimens.

Language: Английский

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Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes.

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

Published: July 5, 2024

Abstract The photopigment-encoding visual opsin genes that mediate colour perception show great variation in copy number and adaptive function across vertebrates. An open question is how this has been shaped by the interaction of lineage-specific structural genomic architecture ecological selection pressures. We contribute to issue investigating expansion dynamics expression duplicated Short-Wavelength-Sensitive-1 (SWS1) sea snakes (Elapidae). generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, 81 SWS1 exon sequences for snakes, analysed these alongside 16 existing genomes their terrestrial relatives. Our analyses revealed multiple independent transitions marine Hydrophis clade, with at least three lineages having intact genes: previously studied cyanocinctus two close relatives species; H. atriceps - fasciatus; an individual curtus . In each lineage, gene divergence a key spectral tuning site resulted distinct UV Violet/Blue-sensitive subtypes. Both variants were simultaneously expressed retinae atriceps, providing first evidence expansions confer novel phenotypes. Finally, chromosome annotation nine species shared features proximity regardless number. If are associated duplication, expanded complements could be more common than currently recognised. Alternatively, pressures specific aquatic environments favour improved chromatic distinction just some lineages. Significance Secondary commonly accompanied pseudogenisation which perception. Conversely, fully-marine hydrophiid snake functionally its short-wavelength-sensitive repertoire following ancestry. current study explores further mapping phylogeny quantifying subtypes within retinae. Despite few reports tetrapods, we provide occurrence events throughout Most intriguingly, spectrally-divergent copies implies functionally-significant phenotype; possibly even trichromacy.

Language: Английский

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Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(8)

Published: July 10, 2024

The photopigment-encoding visual opsin genes that mediate color perception show great variation in copy number and adaptive function across vertebrates. An open question is how this has been shaped by the interaction of lineage-specific structural genomic architecture ecological selection pressures. We contribute to issue investigating expansion dynamics expression duplicated Short-Wavelength-Sensitive-1 (SWS1) sea snakes (Elapidae). generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, 81 SWS1 exon sequences for snakes, analyzed these alongside 16 existing genomes their terrestrial relatives. Our analyses revealed multiple independent transitions marine Hydrophis clade, with at least three lineages having intact genes: previously studied cyanocinctus two close relatives species; atriceps fasciatus; an individual curtus. In each lineage, gene divergence a key spectral tuning site resulted distinct UV Violet/Blue-sensitive subtypes. Both variants were simultaneously expressed retinae H. atriceps, providing first evidence expansions confer novel phenotypes. Finally, chromosome annotation nine species shared features proximity regardless number. If are associated duplication, expanded complements could be more common than currently recognized. Alternatively, pressures specific aquatic environments favor improved chromatic distinction just some lineages.

Language: Английский

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Can All Snakes Swim? A review of the evidence and testing species across phylogeny and morphological diversity

Zoology, Journal Year: 2024, Volume and Issue: 167, P. 126223 - 126223

Published: Oct. 24, 2024

Language: Английский

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Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 2, 2024

Background Animal venom systems have been considered as valuable model for investigating molecular mechanisms underlying phenotypic evolution. The stonefish were reported the most venomous and dangerous fish due to sever human envenomation occasionally fatality, whereas genomic background of their remained under investigated poorly explored compared with other animals. Results In this study, we followed modern venomic pipelines decode Synanceia verrucosa components. A catalog 478 toxin genes annotated based on our assembled chromosome-level genome. Integrative analysis high-quality genome, transcriptome gland proteome crude revealed a mechanism underlined complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit evidenced major source protein production. Further isoform sequencing enabled us uncover massive alternative splicing events total 411 isoforms demonstrated by six genes, further contributing diversity. We then characterized 12 dominantly expressed gland, 11 them produce components, proteins abundant granted. Other included presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, hyaluronidase. Besides, few highly non-toxin also they hypothesized imply housekeeping or hemostasis maintaining roles gland. Notably, gastrotropin like ranked second highest venom, which had never animals, unique property Conclusions results decoded composition verrucosa, highlighted contribution diversity demonstrating tandem-duplication splicing. diverse lethal particles are be pivotal understand adaptive evolution functional studies encouraged exploit components pharmaceutical innovation.

Language: Английский

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Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa

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

Published: Dec. 18, 2024

Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish most venomous and dangerous fish because of severe human envenomation occasionally fatalities, whereas genomic background their has not been fully explored compared with that in other animals. In this study, we followed modern venomic pipelines to decode Synanceia verrucosa components. A catalog 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis high-quality genome, transcriptome gland, proteome crude revealed complexity S. verrucosa. Six tandem-duplicated neoVTX subunit were identified major source protein production. Further isoform sequencing massive alternative splicing events a total 411 isoforms demonstrated by six genes, which further contributed diversity. We then characterized 12 dominantly expressed 11 evidenced produce components, proteins abundant. Other included presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, hyaluronidase. Besides, few highly abundant non-toxin also they hypothesized function housekeeping or hemostasis maintaining roles gland. Notably, gastrotropin like second highest venom, have reported animals contribute unique properties The results composition verrucosa, highlighted contribution diversity through tandem-duplication splicing. diverse lethal particles important understanding adaptive evolution functional studies encouraged exploit components pharmaceutical innovation.

Language: Английский

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