Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(3), P. 519 - 535

Published: Jan. 12, 2024

Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and often assumed to be causally associated with organismal innovations radiations. The 2R hypothesis suggests two WGD events (1R 2R) occurred during early vertebrate evolution. However, the timing of relative divergence gnathostomes (jawed vertebrates) cyclostomes (jawless hagfishes lampreys) unresolved whether these underlie phenotypic diversification remains elusive. Here we present inshore hagfish, Eptatretus burgeri. Through comparative analysis lamprey gnathostome genomes, reconstruct in cyclostome evolution, leveraging insights into ancestral genome. Genome-wide synteny phylogenetic analyses support scenario which 1R stem-lineage Cambrian, stem-lineage, maximally late Cambrian-earliest Ordovician, after its from cyclostomes. We find stem-cyclostomes experienced an additional independent triplication. Functional genomic morphospace demonstrate generally contribute developmental evolution similar changes regulatory both groups. appreciable morphological only but not lineage, calling question general expectation WGDs lead leaps bodyplan complexity.

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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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(10), P. 1493 - 1503

Published: Sept. 30, 2021

How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, updated annotation goldfish chromosome-scale assemblies a progenitor-like diploid Puntius tetrazona outgroup Paracanthobrama guichenoti. Parallel subgenome was featured with equivalent chromosome components, higher protein identities, similar transposon divergence contents, homoeologous exchanges, better synteny level, strong sequence compensation symmetric purifying selection. Furthermore, observed processes allo-tetraploids, including inter-/intrasubgenome trans-splicing events, dominance, decreased levels, dosage compensation, stronger correlation, dynamic functionalization balancing differential expression. The potential disorders introduced by different progenitors were hypothesized be alleviated increasing structural homogeneity performing versatile processes. Resequencing three carp strains revealed major ecotypes uncovered candidate genes relevant growth survival rate.

Language: Английский

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The evolutionary origin and domestication history of goldfish ( Carassius auratus )

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(47), P. 29775 - 29785

Published: Nov. 2, 2020

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% contigs into 50 pseudochromosomes. Comparative genomics enabled us disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative variants 16 wild crucian carp revealed origin identified genomic regions shaped by sweeps linked its domestication. Our comprehensive collection varieties associate genetic variations with number well-known anatomical features, including features distinguish traditional clades. Additionally, tyrosine-protein kinase receptor as candidate causal gene for first case Mendelian inheritance in goldfish-the transparent mutant. The diversity data offer unique resources make promising model functional genomics, well

Language: Английский

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Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(9), P. 1354 - 1366

Published: July 11, 2022

Abstract Triploids are rare in nature because of difficulties meiotic and gametogenic processes, especially vertebrates. The Carassius complex cyprinid teleosts contains sexual tetraploid crucian carp/goldfish ( C. auratus ) unisexual hexaploid gibel carp/Prussian carp gibelio lineages, providing a valuable model for studying the evolution maintenance mechanism polyploids Here we sequence genomes two species assemble their haplotypes, which contain subgenomes (A B), to chromosome level. Sequencing coverage analysis reveals that is an amphitriploid (AAABBB) with triploid sets chromosomes; each set derived from different ancestor. Resequencing data strains show reproduction has been maintained over 0.82 million years. Comparative genomics intensive expansion alterations cell cycle-related genes oocyte-specific histone variant. Cytological assays indicate produces unreduced oocytes by alternative ameiotic pathway; however, sporadic homologous recombination high rate gene conversion also exist . These genomic changes might have facilitated purging deleterious mutations maintaining genome stability this fish. Overall, current results provide novel insights into evolutionary mechanisms reproductive success polyploid

Language: Английский

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A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

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

Published: Sept. 18, 2024

Language: Английский

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Generation of golden goldfish Carassius auratus via tyrosinase gene targeting by CRISPR/Cas9

Aquaculture, Journal Year: 2024, Volume and Issue: 583, P. 740594 - 740594

Published: Jan. 28, 2024

Language: Английский

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Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(8), P. 3383 - 3396

Published: April 14, 2021

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine phenotypes still challenging. Centuries artificial selective breeding for beauty and aggression resulted plethora colors, long-fin varieties, hyper-aggressive behavior air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system studying variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, genome editing, we investigated huge morphological variation fins striking differences coloration fish. Results revealed that double tail, elephant ear, albino, fin spot mutants each were determined by single major-effect loci. The ear phenotype was likely related to differential expression potassium ion channel gene, kcnh8. albinotic linked cis-regulatory element acting on mitfa gene double-tail mutant suggested be caused deletion zic1/zic4 coenhancer. Our data highlight major elements play important roles bringing about innovations establish Bettas as new powerful model study evolved changes.

Language: Английский

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Rodlet cells in kidney of goldfish (Carassius auratus, Linnaeus 1758): A light and confocal microscopy study

Acta Histochemica, Journal Year: 2022, Volume and Issue: 124(3), P. 151876 - 151876

Published: March 15, 2022

Language: Английский

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The genetic basis and potential molecular mechanism of yellow-albino northern snakehead (Channa argus)

Open Biology, Journal Year: 2023, Volume and Issue: 13(2)

Published: Feb. 1, 2023

Body colour is an important economic trait for commercial fishes. Recently, a new morph displaying market-favoured yellow skin (termed as yellow-mutant, YM) of northern snakehead ( Channa argus ) was discovered in China. We confirmed that YM albino with complete loss melanin the and eyes by histological ultrastructural observations, inherited recessive Mendelian trait. By applying genomic analysis approaches, combination gene knockdown rescue experiments, we suggested non-sense mutation slc45a2 (c.383G > A) causation snakehead. Notably, significantly higher levels key melanogenesis genes tyr , tyrp1 dct pmel phospho-MITF protein were detected than those wild-type individuals, underlying mechanism further investigated comparative transcriptomic analysis. Results revealed differential expressed involved pathways like MAPK, WNT calcium signalling induced snakehead, which might account increased amount elements, presumably be stimulated fibroblast-derived melanogenic factors paracrine manner. Our study clarified genetic basis variation C. provided preliminary clue indicating potential involvement fibroblasts pigmentation fish.

Language: Английский

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