African lungfish genome sheds light on the vertebrate water-to-land transition

Cell, Journal Year: 2021, Volume and Issue: 184(5), P. 1362 - 1376.e18

Published: Feb. 5, 2021

Language: Английский

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Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)

Bulletin of the Peabody Museum of Natural History, Journal Year: 2024, Volume and Issue: 65(1)

Published: April 18, 2024

Classification of the tremendous diversity ray-finned fishes (Actinopterygii) began with designation taxonomic groups on basis morphological similarity. Starting in late 1960s phylogenetics became for classification Actinopterygii but failed to resolve many relationships, particularly among lineages within hyperdiverse Percomorpha. The introduction molecular led a dramatic reconfiguration actinopterygian phylogeny. Refined phylogenetic resolution afforded by studies revealed an uneven lineages, resulting proliferation redundant group names Linnean-ranked classifications. Here we provide unranked based summary phylogeny 830 that includes all currently recognized families and 287 fossil taxa. We definitions 90 clade review seven previously defined names. For each 97 names, etymology name, species constituent diagnostic apomorphies, synonyms, discussion clade's nomenclatural systematic history. new is free only one name describe, yielding comprehensive explicitly has emerged 21st century rests foundation previous 200 years research systematics fishes.

Language: Английский

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Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Water Biology and Security, Journal Year: 2021, Volume and Issue: 1(1), P. 100002 - 100002

Published: Nov. 22, 2021

Fish biology has been developed for more than 100 years, but some important breakthroughs have made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent mostly focused genetics, molecular biology, genomics, genome biotechnologies, which provided a solid foundation enhancing aquaculture to ensure food security improving aquatic environments sustain ecosystem health. Here, we review research advances five major areas: (1) biological innovations genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid Asian cyprinid fishes; (2) evolutionary fates consequences natural polyploid (3) domestication selection; (4) development innovation breeding biotechnologies; (5) applicable approaches potential genetic biotechnologies. Moreover, precision biotechniques are examined discussed detail gene editing introgression or removal beneficial detrimental alleles, use sex-specific markers production mono-sex populations, controllable primordial germ cell on-off strategy producing sterile offspring, surrogate broodstock-based strategies accelerate breeding, incorporation sexual regain-based approach create synthetic polyploids. Based these scientific technological advances, propose blueprint improvement new breed creation species analyze seed industry strengthening security.

Language: Английский

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The bowfin genome illuminates the developmental evolution of ray-finned fishes

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(9), P. 1373 - 1384

Published: Aug. 30, 2021

Abstract The bowfin ( Amia calva ) is a ray-finned fish that possesses unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. phylogenetic position as representative neopterygian fishes, its archetypical body plan unduplicated slowly evolving genome make central species for the genomic exploration fishes. Here we present chromosome-level assembly enables gene-order analyses, settling long-debated relationships. We examine chromatin accessibility gene expression through development investigate evolution immune, scale, respiratory fin skeletal systems identify hundreds gene-regulatory loci conserved across vertebrates. These resources connect developmental among bony further highlighting bowfin’s importance illuminating biology diversity in era.

Language: Английский

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Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 19, 2023

Abstract Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play role in survival through mass extinctions. Paddlefish sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to preponderance of duplicate with histories. Here we although there indeed plurality apparently gene duplications, these derive from shared occurring well over 200 million years ago, likely close the Permian-Triassic extinction period. This was followed by prolonged process reversion stable diploid inheritance (rediploidization), have promoted during Triassic-Jurassic extinction. We sharing masked fact paddlefish lineage divergence occurred before rediploidization had proceeded even half-way. Thus, most resolution diploidy lineage-specific. Because only truly duplicated once established, genomes thus mosaic non-shared duplications resulting event.

Language: Английский

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New insights into the evolutionary dynamic and lineage divergence of gasdermin E in metazoa

Frontiers in Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 10

Published: July 22, 2022

Gasdermin (GSDM) is a family of pore-forming proteins that induce pyroptosis. To date, the origin and evolution GSDM in Metazoa remain elusive. Here, we found emerged early Placozoa but absent large number invertebrates. In lower vertebrate, fish, three types GSDME, i.e., GSDMEa, GSDMEb, previously unreported type (designated GSDMEc), were idenitied. Evolutionarily, GSDMEs are distinctly separated: GSDMEa closely related to tetrapod GSDME; GSDMEb exists exclusively fish; GSDMEc forms lineage root GSDMA/B/C/D. shares conserved genomic features with probably prototype GSDMA, which existing all classes. displays fast evolutionary dynamics, likely as result transposition. A cross-metazoan analysis GSDME revealed caspase recognition motif tetrapods cnidarians, whereas has unique similar mammalian GSDMD, exhibits no apparent motif. Through functional test, four highly residues vertebrate proved be essential auto-inhibition. Together our results provide new insights into origin, evolution, function metazoan GSDMs.

Language: Английский

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Teleost swim bladder, an ancient air-filled organ that elicits mucosal immune responses

Cell Discovery, Journal Year: 2022, Volume and Issue: 8(1)

Published: April 5, 2022

The air-filled organs (AOs) of vertebrates (lungs and swim bladders) have evolved unique functions (air-breathing or buoyancy control in water) to adapt different environments. Thus far, immune responses microbes AOs been described exclusively the lungs tetrapods. Similar lungs, bladders (SBs) represent a mucosal surface, feature that leads us hypothesize role for SB immunity. In this study, we demonstrate secretory IgT (sIgT) is key immunoglobulin (Ig) responding viral challenge, only Ig involved neutralization organ. support these findings, found load from fish devoid sIgT was much higher than fish. Interestingly, similar mammals, represents surface with lowest content microbiota. Moreover, main class coating their suggesting homeostasis addition well-established control, our findings reveal previously unrecognized function teleost adaptive upon pathogenic as well unidentified antiviral defense. Overall, indicate despite phylogenetic distance physiological roles mammalian they both analogous against which likely originated independently through process convergent evolution.

Language: Английский

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Single-cell analysis of the amphioxus hepatic caecum and vertebrate liver reveals genetic mechanisms of vertebrate liver evolution

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(10), P. 1972 - 1990

Published: Aug. 16, 2024

Language: Английский

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Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: Sept. 1, 2022

Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction. Anatomical diversity the olfactory organ suggests that olfaction is differentially important among species. To explore this topic, we studied evolutionary dynamics four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) coding for receptors in 185 species ray-finned fishes. The large variation number functional genes, between 28 ocean sunfish Mola mola 1317 reedfish Erpetoichthys calabaricus, result parallel expansions contractions families. Several ancient independent simplifications are associated with massive losses. In contrast, Polypteriformes, which have unique complex organ, almost twice as many receptor genes any other fish. We document link morphology richness repertoire. Further, our results demonstrate genomic underpinning heterogeneous presents dynamic pattern expansions, simplifications, reacquisitions.

Language: Английский

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