Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

Genome Research, Journal Year: 2023, Volume and Issue: 33(9), P. 1527 - 1540

Published: Aug. 17, 2023

Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity chromosome-scale DNA sequences some key taxa. One those limiting taxa has elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes enlarged genomes. Here, we report genome assembly for zebra shark Stegostoma tigrinum, an endangered that a relatively small among sharks (3.71 Gb), as well whale Rhincodon typus Our analysis using male-female comparison identified X Chromosome, first genomically characterized sex chromosome. The Chromosome harbors Hox C cluster whose intact linkage not shown elasmobranch fish. sequenced genomes show gradualism length remarkable length-dependent characteristics-shorter tend to higher GC content, gene density, synonymous substitution rate, simple tandem repeat content smaller lower interspersed content. We challenge traditional binary classification karyotypes without so-called microchromosomes. Even microchromosomes, characteristics persist widely in nonmammalian vertebrates. investigation underpins their unique provides clues understanding how accommodate intragenomic heterogeneity realize complex readout. It also paves way dissecting more variable sizes be at high quality.

Language: Английский

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Connections Across Open Water: A Bi‐Organelle, Genomics‐Scale Assessment of Atlantic‐Wide Population Dynamics in a Pelagic, Endangered Apex Predator Shark (Isurus oxyrinchus)

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 1, 2025

Large-bodied pelagic sharks are key regulators of oceanic ecosystem stability, but highly impacted by severe overfishing. One such species, the shortfin mako shark (Isurus oxyrinchus), a globally widespread, migratory predator, has undergone dramatic population reductions and is now Endangered (IUCN Red List), with Atlantic Ocean in particular assessed fishery managers as overfished need urgent, improved management attention. Genomic-scale assessments for this apex predator species have not been previously available to inform planning; thus, we investigated genetics across using bi-organelle genomics approach. Complete mitochondrial genome (mitogenome) sequences genome-wide SNPs from distributed revealed contrasting patterns structure marker types. Consistent species' long-distance capabilities, showed high connectivity panmixia overall. In contrast, there was matrilineal genetic Northern Southern Hemispheres, suggesting at least large regional-scale female philopatry. Linkage disequilibrium network analysis indicated that makos possess chromosomal inversion occurs wide, feature may be informative evolutionary investigations concerning adaptations global history iconic species. Mitogenome diversity compared other elasmobranchs mitogenome level, nuclear two other, SNPs. These results support efforts on versus Hemisphere scales preserve their distinctiveness. The overall comparative findings provide baseline future monitoring diversity, called United Nations Convention Biological Diversity, cautious optimism regarding health recovery potential if further declines can halted.

Language: Английский

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Stay or go? Space and resource use of the great hammerhead (Sphyrna mokarran) off Andros Island, The Bahamas

Frontiers in Marine Science, Journal Year: 2025, Volume and Issue: 12

Published: March 21, 2025

In light of global declines upper-level marine predators, such as the great hammerhead, ( Sphyrna mokarran) a thorough understanding their behavioral ecology is needed for designing effective management strategies to preserve key role in maintaining ecosystem functioning, stability, and resilience. Within northwestern Atlantic, hammerheads display regional connectivity between U.S. East Coast western edge The Bahamas, but despite suggested importance Bahamian shark sanctuary towards population recovery strategies, relatively few data exist from other areas Bahamas. This study used fisheries-independent drumline captures, satellite telemetry, bulk stable isotope analysis advance our residency, space use, trophic Andros, largest island We examined movement behaviors thermal range within Exclusive Economic Zone, constructed Bayesian mixing models based on carbon, nitrogen, sulfur ratios estimate prey species diet hammerheads. Our revealed year-round residency Andros-caught waters with site-fidelity high use habitats along reef-drop off flats Andros. Great predominantly fed barracuda small-bodied elasmobranchs Andros connecting food webs pelagic zone shoreline. expands knowledge Atlantic shows that, highly-mobile nature, some individuals reside Bahamas year round. These findings suggest could be more than just seasonal refuge this previously proposed, merit further research assess conservation value rebuilding goals greathammerheads.

Language: Английский

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The visual system of the longest-living vertebrate, the Greenland shark

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

Published: April 16, 2025

Abstract The Greenland shark ( Somniosus microcephalus ) is the longest-living vertebrate and inhabits extremely dim cold waters of Arctic deep sea. This has led to speculations that it may have lost functional vision. Here, we present genomic, transcriptomic, histological evidence retains an intact visual system well-adapted for life in light. Histology vitro opsin expression revealed adaptations typical deep-sea species, including densely packed, elongated rods a short-wavelength shift rod pigment sensitivity. RNAscope confirmed presence essential cell types, such as rods, Müller glia, bipolar, amacrine, ganglion cells. Moreover, despite being centuries old, examined specimens showed no signs retinal degeneration. Using whole genome RNA-sequencing, further show dim-light (rod-based) vision genes are robustly expressed, while many bright-light (cone-based) become pseudogenized and/or longer expressed. Finally, our data suggest efficient DNA repair mechanisms contribute long-term preservation function over shark.

Language: Английский

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Comparative genomics illuminates karyotype and sex chromosome evolution of sharks

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(8), P. 100607 - 100607

Published: July 11, 2024

Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow rate chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The common ancestor had proto-vertebrate-like karyotype, including presence 18 microchromosome pairs. X chromosome conversed shared by all suggesting likely origin sex at least 181 million years ago. We characterized Y chromosomes two sharks that are highly differentiated from except small young stratum pseudoautosomal region. found shark lack global dosage compensation dosage-sensitive genes locally compensated. study on evolution enhances our understanding vertebrate evolution.

Language: Английский

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The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catsharkScyliorhinus caniculareveal the molecular bases of sensory organ evolution in jawed vertebrates

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

Published: May 24, 2024

Abstract Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates rays) hold a key phylogenetic position to explore the origin diversifications of jawed vertebrates. Here, we report integrate reference genomic, transcriptomic morphological data in small-spotted catshark Scyliorhinus canicula shed light on evolution sensory organs. We first characterise general aspects genome, confirming high conservation genome organisation across cartilaginous fishes, investigate population genomic signatures. Taking advantage dense sampling data, also identify gene signatures for all major organs, including chondrichthyan specializations, evaluate expression between paralogs within families involved functions. Finally, combine these with 3D synchrotron imaging situ analyses chondrichthyan-specific traits more evolutionary trends systems. This approach brings light, among others, novel markers ampullae Lorenzini electro-sensory cells, duplication hotspot crystallin genes conserved vertebrates, new metazoan clade Transient-receptor potential (TRP) family. These resources results, obtained an experimentally tractable model, open avenues multiomics study

Language: Английский

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The first genetically confirmed live sighting of the Deraniyagala's beaked whale (Mesoplodon hotaula), with insights into the diversity, phylogeny, and past demographic history

Marine Mammal Science, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 5, 2024

Abstract Beaked whales have recently been reported in the South China Sea but with taxonomic uncertainty due to their ambiguous morphological features. Here, we sequenced three genetic markers, control region (CR) and cytochrome b ( cytb ) of mitochondrial genome first intron nuclear muscle actin gene ACTA2 , two biopsy samples collected 2021, revealed unambiguous clustering sequences previously attributed Deraniyagala's beaked whale Mesoplodon hotaula ). Phylogenetic analysis complete mitogenomes strongly supported close relationship between ginkgo‐toothed M. ginkgodens Whole‐genome sequencing suggested a high degree heterozygosity whale. Ancient inbreeding may had greater impact than recent on whales, more are needed draw firm conclusion. The approximate effective population size was found lowest among seven examined ziphiids, which has experiencing steady decline since ~300,000 ya. Therefore, suggest that conservation status should be assessed when essential information is available. results our study provide evidence live sighting fundamental understanding morphological, behavioral, ecological perspectives this cetacean species.

Language: Английский

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The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 6, 2024

Abstract Cartilaginous fishes (chondrichthyans: chimaeras and elasmobranchs -sharks, skates rays) hold a key phylogenetic position to explore the origin diversifications of jawed vertebrates. Here, we report integrate reference genomic, transcriptomic morphological data in small-spotted catshark Scyliorhinus canicula shed light on evolution sensory organs. We first characterise general aspects genome, confirming high conservation genome organisation across cartilaginous fishes, investigate population genomic signatures. Taking advantage dense sampling data, also identify gene signatures for all major organs, including chondrichthyan specializations, evaluate expression between paralogs within families involved functions. Finally, combine these with 3D synchrotron imaging situ analyses chondrichthyan-specific traits more evolutionary trends systems. This approach brings light, among others, novel markers ampullae Lorenzini electro-sensory cells, duplication hotspot crystallin genes conserved vertebrates, new metazoan clade transient-receptor potential (TRP) family. These resources results, obtained an experimentally tractable model, open avenues multiomics study

Language: Английский

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Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(9)

Published: July 3, 2023

Sequenced shark nuclear genomes are underrepresented, with reference available for only four out of nine orders so far. Here, we present the genome, annotations, spiny dogfish (Squalus acanthias), a interest to biomedical and conservation efforts, first representative second largest order sharks (Squaliformes) genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination Illumina paired-end Hi-C sequencing, assembled de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb size, has BUSCO completeness score 91.6%, an error rate less than 0.02%. Annotation predicted 33,283 gene models dogfish's which 31,979 functionally annotated.

Language: Английский

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Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 2, 2024

Abstract Sirenians of the superorder Afrotheria were first mammals to transition from land water and are only herbivorous marine mammals. Here, we generated a chromosome-level dugong ( Dugong dugon ) genome. A comparison our assembly with other afrotherian genomes reveals possible molecular adaptations aquatic life by sirenians, including shift in daily activity patterns (circadian clock) tolerance high-iodine plant diet mediated through changes iodide transporter NIS SLC5A5 its co-transporters. Functional vitro assays confirm that sirenian amino acid substitutions alter properties circadian clock protein PER2 NIS. show evidence convergent regression integumentary system (skin appendages) genes cetaceans. Our analysis also uncovers gene losses may be maladaptive modern environment, candidate KCNK18 for cold stress syndrome likely lost during their evolutionary patterns. Genomes nine Australian locations functionally extinct Okinawan population date genetic break ~10.7 thousand years ago on east coast provide an associated ecotype, highlight need whole-genome resequencing data populations worldwide conservation management.

Language: Английский

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