Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8-6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
Unique evolution of neurohypophysial hormones in cartilaginous fishes: possible implications for urea-based osmoregulation
MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer
Comprehensive survey of carapacial ridge-specific genes in turtle implies co-option of some regulatory genes in carapace evolution
A molecular analysis of neurogenic placode and cranial sensory ganglion development in the shark, Scyliorhinus canicula
Hsp90-inhibitor geldanamycin abrogates G2 arrest in p53-negative leukemia cell lines through the depletion of Chk1
Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?
Into the blue: gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii
Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents
On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species
Evolution of Hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome
Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes
Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys
PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
De novo transcriptome analyses provide insights into opsin-based photoreception in the lanternshark Etmopterus spinax
Evolution of nodal and nodal-related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates
The retinal pigments of the whale shark (Rhincodon typus) and their role in visual foraging ecology.
Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4
Morphological and functional development of the spiral intestine in cloudy catshark (Scyliorhinus torazame).
Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages
Retinal topography and spectral sensitivity of the Port Jackson shark (Heterodontus portusjacksoni).
Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding.
White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability
Mitral cell development in the olfactory bulb of sharks: evidences of a conserved pattern of glutamatergic neurogenesis
'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market
Divergent genes encoding the putative receptors for growth hormone and prolactin in sea lamprey display distinct patterns of expression.
Shark tooth regeneration reveals common stem cell characters in both human rested lamina and ameloblastoma
Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons
Differential expression of myosin heavy chain isoforms in cardiac segments of gnathostome vertebrates and its evolutionary implications
The retinal pigments of the whale shark (Rhincodon typus) and their role in visual foraging ecology-CORRIGENDUM.
New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts.
Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception.
Lost structural and functional inter-relationships between Ig and TCR loci in mammals revealed in sharks.
The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish
A method for making alignments of related protein sequences that share very little similarity; shark interleukin 2 as an example.
Developmental fates of shark head cavities reveal mesodermal contributions to tendon progenitor cells in extraocular muscles.
RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data.
Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus)
Composition of uterine milk and its changes with gestational period in red stingrays (Hemitrygon akajei).
Not just shades of grey: life is full of colour for the ocellate river stingray (Potamotrygon motoro).
Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles.
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