Molecular Ecology Resources, Год журнала: 2023, Номер 24(1)
Опубликована: Дек. 14, 2023
Annual Review of Animal Biosciences, Год журнала: 2023, Номер 12(1), С. 233 - 259
Опубликована: Окт. 20, 2023
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so that even closely related species often differ in systems. Teleost fish a taxonomic group with frequent turnovers of sex-determining and thus provides us great opportunities to investigate the molecular evolutionary underlying turnover Here, we compile recent studies on diversity fish. We demonstrate genes TGF-β signaling pathway frequently used for master (MSD) genes. MSD arise via two main mechanisms, duplication-and-transposition allelic mutations, few exceptions. also temperature influences sex determination many species, those chromosomes, higher temperatures inducing differentiation into males most cases. Finally, review theoretical models discuss what questions remain elusive.
Язык: Английский
Процитировано
43
Aquaculture, Год журнала: 2024, Номер 583, С. 740589 - 740589
Опубликована: Янв. 17, 2024
Genomics is increasingly applied in breeding programmes for farmed fish and shellfish species around the world. However, current applications do not include information on genome functional activity, which can enhance opportunities to predict relationships between genotypes phenotypes hence increase accuracy of selection. Here, we review prospects improving aquaculture practises through uptake genomics data light EU Horizon 2020 project AQUA-FAANG: ‘Advancing European Aquaculture by Genome Functional Annotation’. This consortium targeted six major aquaculture, producing thousands genomic datasets from samples representing embryos mature adults both sexes, following immunological stimulation. was used catalogue activity across each species, revealing transcribed regions, distinct chromatin states regulatory elements impacting gene expression. These annotations were shared as open Ensembl browser using latest reference genomes species. AQUA-FAANG offers novel identify prioritize causative genetic variants responsible diverse traits including disease resistance, be exploited selective breeding. Such knowledge associated resources have potential improve sustainability boost production accelerating gain health robustness infection, whilst reducing requirement animal testing. We further outline directions advance leverage annotation beyond project. Given diversity sectors businesses, incorporation into decisions will depend technological readiness level scale operation, with cost-benefit analysis necessary determine most profitable approach system.
Язык: Английский
Процитировано
13
Nature Reviews Genetics, Год журнала: 2024, Номер unknown
Опубликована: Июль 18, 2024
Язык: Английский
Процитировано
12
Aquatic Toxicology, Год журнала: 2024, Номер 273, С. 107022 - 107022
Опубликована: Июль 14, 2024
Язык: Английский
Процитировано
4
Biomolecules, Год журнала: 2025, Номер 15(1), С. 54 - 54
Опубликована: Янв. 2, 2025
Fish exhibit diverse mechanisms of sex differentiation and determination, shaped by both external internal influences, often regulated distinct DNA methylation patterns responding to environmental changes. In S. senegalensis aquaculture, reproductive issues in captivity pose significant challenges, particularly the lack fertilization capabilities captive-bred males, hindering genetic improvement measures. This study analyzed transcriptomic profiles gonadal tissue from groups differing rearing conditions sexual maturity stages. RRBS (Reduced Representation Bisulfite Sequencing) was employed detect notable variations across groups, while RNA extracted sequenced for differential expression analysis. Our findings suggest that significantly regulates gene expression, acting as a mechanism can repress enhance depending on genomic context. The complexity this epigenetic is evident varying levels correlation rates observed different CpGs neighboring specific genes linked reproduction. Differential comparisons revealed highest number differently methylated between maturation stages, followed conditions, lastly sexes. These underscore crucial role regulating its potential differentiation, highlighting complex interplay modifications expression.
Язык: Английский
Процитировано
0
BMC Biology, Год журнала: 2025, Номер 23(1)
Опубликована: Март 11, 2025
Abstract Background Viral nervous necrosis (VNN) is an important viral disease threatening global aquaculture sustainability and affecting over 50 farmed ecologically fish species. A major QTL for resistance to VNN has been previously detected in European sea bass, but the underlying causal gene(s) mutation(s) remain unknown. To identify mechanisms genetic factors underpinning we employed integrative analyses of multiple functional genomics assays bass. Results The estimated heritability was high ( h 2 ~ 0.40), a explaining up 38% variance trait confirmed on chromosome 3, with individuals resistant genotype showing 90% survivability against outbreak. Whole-genome resequencing narrowed location this small region containing 4 copies interferon alpha inducible protein 27-like 2A IFI27L2A ) genes, one copy IFI27L2 gene. RNA sequencing revealed clear association between expression two Integration chromatin accessibility histone modification data pinpointed SNPs active regulatory regions these genes ), transcription factor binding site gains alleles were predicted. These alleles, particularly SNP variant CHR3:10,077,301, exhibited higher frequencies (0.55 0.77) Eastern Mediterranean Sea bass populations, which show considerably levels VNN, as compared susceptible West Atlantic populations (0.15–0.25). Conclusions through modulation likely causative mutation This first mutations discovered traits paves way marker-assisted selection well biotechnological approaches enhance other
Язык: Английский
Процитировано
0
International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(7), С. 3282 - 3282
Опубликована: Апрель 1, 2025
The canonical model of vertebrate sex chromosome evolution predicts a one-way trend toward degradation. However, most chromosomes in lower vertebrates are homomorphic. Recent progress studies determination has resulted the discovery more than 30 master (MSD) genes, which from teleost fish. An analysis MSD gene acquisition, recombination suppression, and chromosome-specific sequences revealed correlations modes acquisition chromosomes. Sex remain homomorphic with genes acquired by simple mutations, duplications, allelic variations, or neofunctionalization; contrast, they become heteromorphic chromosomal inversion, fusion, fission. There is no suppression carrying gained through mutations. In there extensive inversion. limited transposition translocation. We propose cause-effect that as consequence explains various vertebrates. A key factor determining whether non-homologous regions created during genes. Chromosome inversion creates inversely homologous but directly sequences, lead to retain potential. Over time, recurrent inverted leads formation strata may cause degradation Depending on nature deletions regions, evolve dosage compensation, selective retention haplo-insufficient be used an alternative strategy.
Язык: Английский
Процитировано
0
Frontiers in Marine Science, Год журнала: 2025, Номер 12
Опубликована: Май 30, 2025
Introduction Compared to mammals and birds, sex-determining genes differ in most fish species. Largemouth bass ( Micropterus Salmoides ) is one of the important cultured species China, there are growth differences between males females. However, its mechanisms currently remain unknown. Methods We explored sex-determination mechanism by integrating whole-genome sequencing, resequencing comparative genomics approaches. Results In this study, we employed HiFi Hi-C sequencing technologies construct a chromosome-level haplotypic genome assembly for male largemouth bass, with size 875.69 Mb. The assembled contains 23 chromosomes, covering 95.31% complete sequences high scaffold N50 35.93 A genome-wide association study (GWAS) sex was performed four populations consisting 62 58 For trait, total 3,838 SNP loci were identified be significantly associated sexual discrepancy. Interestingly, almost all these significant SNPs (3,825) clustered on chromosome 10 (Chr10), within 3.5-Mb region (SDR). They homozygous females while heterozygous males. therefore speculate that owns XX/XY determination system. By comparing data examining coverage depth reads, revealed ~51-kb male-specific (MSR) Chr10. Gene annotation discovered coding sequence msy MSR-1, which may contribute bass. differential expression analysis, two candidate ccdc103 jockey predicted target SDR. Moreover, applied non-coding fragments (within MSR-2 MSR-3) design specific markers, successfully obtaining universal gender identity examined Discussion Overall, our findings improve understanding molecular basis will thereby promote mono-sexual breeding progress aquaculture industry.
Язык: Английский
Процитировано
0
Scientific Data, Год журнала: 2024, Номер 11(1)
Опубликована: Ноя. 4, 2024
Abstract The olive flounder, Paralichthys olivaceus , also known as the Korean halibut, is an economically important flatfish in East Asian countries. Here, we provided four fully phased genome assemblies of two different flounder individuals using high-fidelity long-read sequencing and their parental short-read data. We obtained 42–44 Gb ~15-kb ~Q30 long reads, assembly quality values were ~53. annotated ~30 K genes, ~170-Mb repetitive sequences, ~3 M 5-methylcytosine positions for each assembly, established a graph-based draft pan-genome flounder. identified 5 single-nucleotide variants 100 structural with genotype information, where ~13% possibly fixed individuals. Based on our chromosome-level explored chromosome evolution Pleuronectiformes family, reported earlier. Our high-quality genomic resources will contribute to future selection accelerating breeding process
Язык: Английский
Процитировано
3
Genomics, Год журнала: 2024, Номер 116(2), С. 110802 - 110802
Опубликована: Янв. 28, 2024
Understanding vertebral bone development is essential to prevent skeletal malformations in farmed fish related genetic and environmental factors. This an important issue Solea senegalensis, with special impact of spinal anomalies postlarval juvenile stages. Vertebral transcriptomics mainly comes from coding genes, barely on miRNA expression. Here, we used RNA-seq samples obtain the first comprehensive transcriptomic repertoire for bone, covering different phenotypes egg-incubation temperatures skeleton health S. senegalensis. Coding pathways regulating growth were identified. Differential profiles suggestive mRNA-miRNA interactions found between postlarvae juveniles. Bone-related genes functions associated extracellular matrix, regulatory processes, calcium binding, retinol lipid metabolism or response stimulus, including those revealed by targets signaling, cellular metabolic growth, cell proliferation biological adhesion. Pathway enrichment identified when comparing juveniles: postlarvae, while actin cytoskeleton, focal adhesion proteasome remodeling The transcriptome data disclosed candidate gene markers references functional studies anosteocytic study establishes a broad foundation healthy anomalous spines under early thermal conditions across life-stages comparative analysis homeostasis pathology vertebrates.
Язык: Английский
Процитировано
1