The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

Nature Ecology & Evolution, Год журнала: 2020, Номер 4(6), С. 841 - 852

Опубликована: Март 30, 2020

Abstract Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it a key phylogenetic position at the base ~30,000 modern teleost species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities investigate evolution polyploid genomes. We assembled high-quality chromosome-level reference genome for sterlet, Acipenser ruthenus . Our analysis revealed very low protein rate that is least as slow other deep branches vertebrate tree, such coelacanth. uncovered whole-genome duplication occurred Jurassic, early entire sturgeon lineage. Following polyploidization, rediploidization included loss whole chromosomes segmental deduplication process. While known adaptive processes helped conserve high degree structural and functional tetraploidy over more than 180 million years, reduction redundancy seems have been remarkably random.

Язык: Английский

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The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Окт. 11, 2019

Abstract Common carp ( Cyprinus carpio ) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. compare related diploid Cyprinid genomes. We identify Barbinae lineage as potential progenitor then divide the into two subgenomes marked by distinct similarity progenitor. estimate that progenitors diverged around 23 Mya merged 12.4 based on divergence rates homoeologous genes transposable elements subgenomes. No extensive gene losses are observed either subgenome. Instead, find expression bias across surveyed tissues such subgenome B more dominant expression. CG methylation promoter regions may play important role altering .

Язык: Английский

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The hagfish genome and the evolution of vertebrates

Nature, Год журнала: 2024, Номер 627(8005), С. 811 - 820

Опубликована: Янв. 23, 2024

Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution 1–3 . Here we investigate complex history, timing functional role genome-wide duplications 4–7 programmed DNA elimination 8,9 in vertebrates light chromosome-scale genome sequence for brown hagfish Eptatretus atami Combining evidence from syntenic phylogenetic analyses, establish comprehensive picture evolution, including an auto-tetraploidization (1R V ) that predates Cambrian cyclostome–gnathostome split, followed by mid–late allo-tetraploidization (2R JV gnathostomes prolonged Cambrian–Ordovician hexaploidization CY cyclostomes. Subsequently, underwent extensive genomic changes, with chromosomal fusions accompanied loss genes are essential organ systems (for example, involved development eyes proliferation osteoclasts); these changes account, part, simplification body plan 1,2 Finally, characterize hagfish, identifying protein-coding repetitive elements deleted somatic cell during development. The germline-specific provides mechanism resolving genetic conflict between soma germline repressing pluripotency functions, paralleling findings 10,11 Reconstruction history framework further investigations cyclostomes jawed vertebrates.

Язык: Английский

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Research advances in the genomics and applications for molecular breeding of aquaculture animals

Aquaculture, Год журнала: 2020, Номер 526, С. 735357 - 735357

Опубликована: Апрель 10, 2020

Язык: 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, Год журнала: 2021, Номер 1(1), С. 100002 - 100002

Опубликована: Ноя. 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.

Язык: Английский

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

Nature Genetics, Год журнала: 2021, Номер 53(10), С. 1493 - 1503

Опубликована: Сен. 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.

Язык: Английский

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From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish

Science Advances, Год журнала: 2020, Номер 6(22)

Опубликована: Май 27, 2020

A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence plants. Although animal polyploids are thought experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates ~15 million years ago. Comprehensive analyses identify changes subgenomic evolution from asymmetrical oscillation common carp diverse stabilization balanced gene expression continuous rediploidization. The homoeologs coexpressed most pathways, their dominance shifts temporally embryogenesis. Homoeolog correlates negatively with alternation DNA methylation. results show that cyprinids have a unique strategy balancing diversification. Rediploidization process these fishes provides intriguing insights into function allopolyploid vertebrates.

Язык: Английский

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

Proceedings of the National Academy of Sciences, Год журнала: 2020, Номер 117(47), С. 29775 - 29785

Опубликована: Ноя. 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

Язык: Английский

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AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 119(1)

Опубликована: Дек. 21, 2021

Significance One fundamental analysis needed to interpret genome assemblies is alignment. Yet, accurately aligning regulatory and transposon regions outside of genes remains challenging. We introduce Anchored Wavefront alignment (AnchorWave), which implements a duplication informed longest path algorithm identify collinear performs base pair–resolved, end-to-end for blocks using an efficient two-piece affine gap cost strategy. AnchorWave improves the under number scenarios: genomes with high similarity, large transposable element activity, many inversions, alignments between species deeper evolutionary divergence different whole-genome histories. Potential use cases include comparison nongenic sequences population genetics taxa large, repeat-rich genomes.

Язык: Английский

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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Nature Genetics, Год журнала: 2022, Номер 54(7), С. 1037 - 1050

Опубликована: Июль 1, 2022

Zebrafish, a popular organism for studying embryonic development and modeling human diseases, has so far lacked systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium created central repository store process zebrafish developmental genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines total of 1,802 sets unpublished re-analyzed published data, which used improve existing annotations show its utility experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity time space. delineated distance topology chromatin between regulatory active during zygotic genome activation organogenesis. Finally, matched epigenomic landscapes mouse predicted relationships them beyond sequence similarity, thus extending genomics mammals.

Язык: Английский

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