Haplotype-resolved assembly of diploid genomes without parental data

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(9), P. 1332 - 1335

Published: March 24, 2022

Language: Английский

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Giant lungfish genome elucidates the conquest of land by vertebrates

Nature, Journal Year: 2021, Volume and Issue: 590(7845), P. 284 - 289

Published: Jan. 18, 2021

Abstract Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ land and ultimately gave rise all vertebrates, including humans 1–3 . Here we determine chromosome-quality genome of Australian lungfish ( Neoceratodus forsteri ), which is known have largest any animal. The vast size this genome, about 14× larger than that humans, attributable mostly huge intergenic regions introns with high repeat content (around 90%), components resemble those tetrapods (comprising mainly long interspersed nuclear elements) more they do ray-finned fish. continues expand independently (its transposable elements are still active), through mechanisms different enormous genomes salamanders. 17 fully assembled macrochromosomes maintain synteny other vertebrate chromosomes, microchromosomes conserved ancient homology ancestral karyotype. Our phylogenomic analyses confirm previous reports occupy a key evolutionary position as closest living relatives 4,5 , underscoring importance for understanding innovations associated terrestrialization. Lungfish preadaptations on include gain limb-like expression developmental genes such hoxc13 sall1 their lobed fins. Increased rates evolution duplication obligate air-breathing, lung surfactants expansion odorant receptor gene families (which encode proteins involved detecting airborne odours), contribute tetrapod-like biology lungfishes. These findings advance our major transition during evolution.

Language: Английский

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Sex determination mechanisms and sex control approaches in aquaculture animals

Science China Life Sciences, Journal Year: 2022, Volume and Issue: 65(6), P. 1091 - 1122

Published: May 16, 2022

Language: Английский

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Genome assembly in the telomere-to-telomere era

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(9), P. 658 - 670

Published: April 22, 2024

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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Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

Cell, Journal Year: 2021, Volume and Issue: 184(5), P. 1377 - 1391.e14

Published: Feb. 5, 2021

Language: Английский

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A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1832), P. 20200089 - 20200089

Published: July 12, 2021

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change master determination gene, chromosome or system (e.g. XY to WZ). Jumping genes stay main triggers but translocate other chromosomes. Occasional recombination sex-reversed females) prevents degeneration. Recent research has uncovered conserved heteromorphic even homomorphic several clades non-avian and non-mammalian Sex sturgeons (Acipenseridae) been a long-standing basic biological question, linked economical demands by caviar-producing aquaculture. Here, we report discovery sex-specific sequence from sterlet ( Acipenser ruthenus ). Using chromosome-scale assemblies pool-sequencing, first identified an approximately 16 kb female-specific region. We developed PCR-genotyping test, yielding products six species, spanning entire phylogeny with most divergent extant lineages A. sturio, oxyrinchus versus ruthenus, Huso huso ), stemming ancient tetraploidization. Similar results were obtained two octoploid species gueldenstaedtii, baerii Conservation for long period, representing 180 Myr sturgeon evolution, across at least one polyploidization event, raises many interesting questions. discuss ZZ/ZW-mode potential alternatives. This article is part theme issue ‘Challenging paradigm evolution: empirical theoretical insights focus on vertebrates (Part I)’.

Language: Английский

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Genomic selection and its research progress in aquaculture breeding

Reviews in Aquaculture, Journal Year: 2022, Volume and Issue: 15(1), P. 274 - 291

Published: Aug. 1, 2022

Abstract Since its introduction in 2001, genomic selection (GS) has progressed rapidly. As a research and application hot topic, GS led to revolution the field of animal plant breeding. Thanks ability overcome shortcomings traditional breeding methods, garnered increasing attention. Both theoretical practical studies have revealed higher accuracy than that breeding, which can accelerate genetic gain. In recent years, many been conducted on aquaculture species, shown produces prediction pedigree‐based method. The present study reviews principles processes, preconditions, advantages, analytical methods factors influencing as well progress into these aspects. Furthermore, future directions are also discussed, should expand more species.

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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Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(7), P. 3542 - 3542

Published: March 24, 2022

DNA replication during cell proliferation is ‘vertical’ copying, which reproduces an initial amount of genetic information. Polyploidy, results from whole-genome duplication, a fundamental complement to vertical copying. Both organismal and polyploidy can emerge via premature cycle exit or cell-cell fusion, the latter giving rise polyploid hybrid organisms epigenetic hybrids somatic cells. Polyploidy-related increase in biological plasticity, adaptation, stress resistance manifests evolution, development, regeneration, aging, oncogenesis, cardiovascular diseases. Despite prevalence nature importance for medicine, agri- aquaculture, processes mechanisms underlying these features largely remain unknown. The evolutionarily conserved include activation transcription, response stress, damage hypoxia, induction programs morphogenesis, unicellularity, longevity, suggesting that common confer adaptive viability, cells organisms. By increasing polyploidization provide survival under stressful conditions where diploid cannot survive. However, it occurs at expense specific function, thus promoting developmental programming adult diseases risk cancer. Notably, genes arising evolutionary are heavily involved cancer other Ploidy-related changes gene expression presumably originate chromatin modifications derepression bivalent genes. provided evidence elucidates role carcinogenesis, may contribute development new strategies regeneration preventing

Language: Английский

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