Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish

Nature Ecology & Evolution, Год журнала: 2022, Номер 6(9), С. 1354 - 1366

Опубликована: Июль 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

Язык: Английский

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Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Frontiers in Genetics, Год журнала: 2022, Номер 13

Опубликована: Ноя. 2, 2022

Major progress has been made with genomic and genetic studies in aquaculture the last decade. However, research on epigenetic regulation of traits is still at an early stage. It apparent that most, if not all, are regulated both levels. This paper reviews recent understanding important such as growth, reproduction, disease resistance, stress responses. Although it challenging to make generalized statements, DNA methylation mostly correlated down-regulation gene expression, especially when promoters enhancers. As such, growth factors their receptors negatively growth; hypomethylation genes for tolerance increased tolerance; male or female sex differentiation leads into males females, respectively. environmental mediated level regulation, environment-induced changes appeared be intergenerationally inherited, but evidences transgenerational inheritance limited.

Язык: Английский

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Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution

BMC Genomics, Год журнала: 2022, Номер 23(1)

Опубликована: Апрель 7, 2022

The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well unique body plan environmental adaptation.We assembled the chromosome-level genome using PacBio sequencing chromosome structure capture technique. final assembly a total length of 893.2 Mb with contig N50 19.3 scaffold 35.7 Mb. About 99.85% contigs were anchored into 24 chromosomes. Based on prediction, contained 30,342 protein-coding genes 43.26% repetitive sequences. Furthermore, we determined that large size can be attributed to DNA-mediated transposable elements which accounted for 58.9% sequences in carp. We identified only pairs chromosomes due fusion two ancestral Enrichment analyses significantly expanded positively selected reflected adaptation feeding habits. also detected loss conserved non-coding regulatory associated development immune system, nervous digestive may critical herbivorous traits.The high-quality reference reported here provides valuable resource genetic improvement molecular-guided breeding

Язык: Английский

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The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation

Developmental Cell, Год журнала: 2023, Номер 58(2), С. 155 - 170.e8

Опубликована: Янв. 1, 2023

In anamniote embryos, the major wave of zygotic genome activation starts during mid-blastula transition. However, some genes escape global repression, are activated substantially earlier, and contribute to minor activation. The mechanisms underlying little understood. We explored genomic organization cis-regulatory a transcription body, in which is first detected zebrafish. identified miR-430 cluster as having excessive copy number highest density Pol-II-transcribed promoters genome, this required for forming body. body not essential for, nor does it encompasse, globally. Instead, distinct minor-wave-specific promoter architecture suggests that promoter-autonomous regulate features also suggest initiation between waves

Язык: Английский

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The Genetic Basis of Morphological Diversity in Domesticated Goldfish

Current Biology, Год журнала: 2020, Номер 30(12), С. 2260 - 2274.e6

Опубликована: Май 8, 2020

Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these is poorly understood. Here, based on analysis of transposable elements allotetraploid genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event ancestor and common carp. We conducted sequencing 27 wild goldfish. identified more than 60 million variations established population structure major strains. Genome-wide association studies strain-specific variants revealed loci associated with several phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, heart-shaped tail. Our results suggest accumulated mutations led to generation diverse domestication history. This study key resource for understanding phenotypic diversity among

Язык: Английский

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The Pharus latifolius genome bridges the gap of early grass evolution

The Plant Cell, Год журнала: 2021, Номер 33(4), С. 846 - 864

Опубликована: Янв. 15, 2021

The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. ancestry of genomes shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance ρ-WGD remains elusive. We sequenced genome Pharus latifolius, species (producing true spikelet) subfamily Pharoideae, sister lineage core Poaceae including (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae (PACMAD) Bambusoideae, Oryzoideae, Pooideae (BOP) clades. Our results indicate that P. latifolius has evolved slowly relative genomes, as reflected by moderate rates molecular evolution, limited chromosome rearrangements low rate gene loss for duplicated genes. show event occurred approximately 98.2 million years ago (Ma) common ancestor Pharoideae PACMAD BOP grasses. This was followed contrasting patterns diploidization lineages. presence two FRIZZY PANICLE-like genes MADS-box genes, support hypothesis may have played role origin functional diversification spikelet, an adaptation grasses related directly yields. sheds light on early evolution underpinning biology breeding cereals.

Язык: Английский

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Partitioning of gene expression among zebrafish photoreceptor subtypes

Scientific Reports, Год журнала: 2021, Номер 11(1)

Опубликована: Авг. 30, 2021

Abstract Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- bright-light vision, respectively. While many molecular features that distinguish cones known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes renowned the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult in zebrafish, a teleost. We found addition four canonical zebrafish types, there exist subpopulations green red (previously shown be located ventral retina) express red-shifted opsin paralogs ( opn1mw4 or opn1lw1 ) as well unique combination phototransduction genes. Furthermore, paralogous genes is partitioned subtypes, analogous partitioning between seen across vertebrates. The cone-gene pairs arose via teleost-specific whole-genome duplication later clade-specific duplications. also discovered distinct transcriptional regulators, including factors not previously implicated development differentiation. Overall, our work suggests action differentially expressed regulators enables diversification teleosts.

Язык: Английский

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Mast cells in goldfish (Carassius auratus) gut: Immunohistochemical characterization

Acta Zoologica, Год журнала: 2022, Номер 104(3), С. 366 - 379

Опубликована: Март 1, 2022

Abstract The common goldfish is the most widespread teleosts in world. Due to its peculiar characteristics, such as high resistance, easy availability and stabulation, for evolutionary this fish lends itself be one of used experimental models. This study aimed characterize mast cells intestine Carassius auratus using anti‐TLR‐2, anti‐S100, anti‐VIP, anti‐serotonin (5‐HT) anti‐Piscidin antibodies. goldfish, like that all vertebrates, plays an important role immunology animal. gut‐associated lymphoid tissue GALT immune component containing several specific lymphocytes, macrophages cells. In addition, presence goblet intestinal epithelium strengthens defence system, secreting many cytokines chemokines displaying antibacterial properties. Our results show labelled with antibodies are highly conserved between mammals, demonstrating active these response.

Язык: Английский

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Genomic consequences of domestication of the Siamese fighting fish

Science Advances, Год журнала: 2022, Номер 8(10)

Опубликована: Март 9, 2022

Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but genetic bases of their domestication phenotypic diversification largely unknown. We assembled de novo genome a wild Betta splendens whole-genome sequenced 98 individuals across five closely related species. find evidence bidirectional hybridization between domesticated ornamental betta other discover dmrt1 as main sex determination gene in that it has lower penetrance B. . Furthermore, we genes with signatures recent, strong selection have large effects on color specific parts body or shape individual fins unlinked. Our results demonstrate how simple architectures paired anatomical modularity can lead to vast diversity generated during animal launch powerful new system for evolutionary genetics.

Язык: Английский

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Transposon signatures of allopolyploid genome evolution

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июнь 1, 2023

Abstract Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, allopolyploidy, allows these to persist as subgenomes during subsequent meioses. Here, we present a general method for identifying the of polyploid based on shared ancestry revealed by genomic distribution repetitive elements that were active in progenitors. This subgenome-enriched transposable element signal is intrinsic polyploid, allowing broader applicability than other approaches depend availability sequenced diploid relatives. We develop statistical basis method, demonstrate its well-studied cases tobacco, cotton, and Brassica napus , apply it several cases: allotetraploid cyprinids, allohexaploid false flax, allooctoploid strawberry. These analyses provide insight into origins polyploids, revise subgenome identities strawberry, perspective dominance higher polyploids.

Язык: Английский

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