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Knowledge about paternal-effect-genes (PEGs) (genes whose expression in the progeny is influenced by paternal factors present in the sperm) in fish is very limited. To explore this issue, we used milt cryopreservation as a specific challenge test for sperm cells, thus enabling selection amidst cryo-sensitivity. We created two groups of Eurasian perch ( Perca fluviatilis ) as a model – eggs fertilized either with fresh (Fresh group) or cryopreserved (Cryo group) milt from the same male followed by phenotypic-transcriptomic examination of consequences of cryopreservation in obtained progeny (at larval stages). Most of the phenotypical observations were similar in both groups, except the final weight which was higher in the Cryo group. Milt cryopreservation appeared to act as a \"positive selection\" factor, upregulating most PEGs in the Cryo group. Transcriptomic profile of freshly hatched larvae sourced genes involved in the development of visual perception and we identified them as PEGs. Consequently, larvae from the Cryo group exhibited enhanced eyesight, potentially contributing to more efficient foraging and weight gain compared to the Fresh group. This study unveils, for the first time, the significant influence of the paternal genome on the development of the visual system in fish, highlighting pde6g , opn1lw1 , and rbp4l as novel PEGs.

Domestication is an evolutionary process during which we expect populations to progressively adapt to an environment controlled by humans. It is accompanied by genetic and presumably epigenetic changes potentially leading to modifications in the transcriptomic profile in various tissues. Reproduction is a key function often affected by this process in numerous species, regardless of the mechanism. The maternal mRNA in fish eggs is crucial for the proper embryogenesis. Our working hypothesis is that modifications of maternal mRNAs may reflect potential genetic and/or epigenetic modifications occurring during domestication and could have consequences during embryogenesis. Consequently, we investigated the trancriptomic profile of unfertilized eggs from two populations of Eurasian perch. These two populations differed by their domestication histories (F1 vs. F7+–at least seven generations of reproduction in captivity) and were genetically differentiated (FST = 0.1055, p<0.05). A broad follow up of the oogenesis progression failed to show significant differences during oogenesis between populations. However, the F1 population spawned earlier with embryos presenting an overall higher survivorship than those from the F7+ population. The transcriptomic profile of unfertilized eggs showed 358 differentially expressed genes between populations. In conclusion, our data suggests that the domestication process may influence the regulation of the maternal transcripts in fish eggs, which could in turn explain differences of developmental success.

Abstract Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis , Perca schrenkii , and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. Results We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene ( amhr2bY ), previously suggested to be the master sex-determining (MSD) gene in P. flavescens . Phylogenetically related and structurally similar a mhr2 duplicates ( amhr2b ) were found in P. schrenkii and Sander lucioperca , potentially dating this duplication event to their last common ancestor around 19–27 Mya. In P. fluviatilis and S. vitreus , this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca . Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens . In P. fluviatilis , a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three ( c18h1orf198 , hsdl1 , tbc1d32 ) with higher expression in the testis than in the ovary. Conclusions Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in , and along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene ( ), previously suggested to be the master sex determining (MSD) gene in . Phylogenetically related and structurally similar a duplications ( ) were found in and , potentially dating this duplication event to their last common ancestor around 19-27 Mya. In and , this duplicate has been lost while it was subject to amplification in . Analyses of the locus in suggest that this duplication could be also male-specific as it is in . In , a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three ( , , ) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known species.

Knowledge about paternal-effect genes (the expression of which in progeny is controlled by the paternal genome) in fish is very limited. To explore this issue, we used semen cryopreservation as a specific challenge test for sperm cells, thus enabling selection amidst cryo-sensitivity. We created two groups of Eurasian perch (Perca fluviatilis) as a model - eggs fertilized either with fresh (Fresh group) or cryopreserved (Cryo group) semen from the same male followed by zootechnical-transcriptomic examination of consequences of cryopreservation in obtained progeny (at larval stages). Most of the zootechnical observations were similar in both groups, except the final weight was higher in the Cryo group. Semen cryopreservation appeared to act as a \"positive selection\" factor, upregulating most paternal-effect genes in the Cryo group. Transcriptomics profile of freshly hatched larvae sourced genes involved in the development of visual perception as paternal-effect genes. Consequently, larvae from the Cryo group exhibited enhanced eyesight, potentially contributing to more efficient foraging and weight gain compared to the Fresh group. This study unveils, for the first time, the significant influence of the paternal genome on the development of the visual system in fish, highlighting pde6g, opn1lw1, and rbp4l as novel paternal-effect genes.Competing Interest StatementThe authors have declared no competing interest.

Transcriptomic analysis of freshly hatched fish larvae offers insights into phenotype development, yet it remains uncertain whether it reflects parental influence or predicts individual growth. This research scrutinizes the transcriptome of 16 Eurasian perch (Perca fluviatilis) larval groups alongside pre- and post-hatching traits. Despite consistent fertilization rates, significant variations in embryonic development and larval performance highlight diverse phenotypes studied. It enabled to bring our attention to the fact that larval transcriptome can serve as a window into both the parental contributions and the future performance of the larvae. Our further analysis shed light on ribosome biogenesis, neurogenesis, and the cell cycle, as important processes shaping early larval performance. Additionally, we propose a set of predictive, validated gene markers associated with further larval performance and key aquaculture traits, such as selenoo (associated with cannibalism), trim16 (fulton’s condition factor), slc15a1 (specific growth factor), and cipc (final weight). This study delves into the descriptive and predictive nature of the transcriptomic portrait of newly hatched larvae, paving the way to comprehend the intricate developmental pathways from fertilization towards juvenile stage.

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore ( Bos indicus ) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis -regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis -regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3′UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.

Data from the general population suggest that fatality rates declined during the course of the pandemic. This analysis, using data extracted from the Brazilian Kidney Transplant COVID-19 Registry, seeks to determine fatality rates over time since the index case on March 3rd, 2020. Data from hospitalized patients with RT-PCR positive SARS-CoV-2 infection from March to August 2020 (35 sites, 878 patients) were compared using trend tests according to quartiles (Q1: <72 days; Q2: 72–104 days; Q3: 105–140 days; Q4: >140 days after the index case). The 28-day fatality decreased from 29.5% (Q1) to 18.8% (Q4) ( p for-trend = 0.004). In multivariable analysis, patients diagnosed in Q4 showed a 35% reduced risk of death. The trend of reducing fatality was associated with a lower number of comorbidities (20.7–10.6%, p for-trend = 0.002), younger age (55–53 years, p for-trend = 0.062), and better baseline renal function (43.6–47.7 ml/min/1.73 m 2 , p for-trend = 0.060), and were confirmed by multivariable analysis. The proportion of patients presenting dyspnea ( p for-trend = 0.001) and hypoxemia ( p for-trend < 0.001) at diagnosis, and requiring intensive care was also found reduced ( p for-trend = 0.038). Despite possible confounding variables and time-dependent sampling differences, we conclude that COVID-19-associated fatality decreased over time. Differences in demographics, clinical presentation, and treatment options might be involved.

(1) Background: Nanocrystals (NCs)-based electrochemical sensors have been proposed for biomarkers detection, although immunosensors using ZnO NCs decorated with copper are still scarce. (2) Methods: Electrochemical immunodetection of human salivary alpha-amylase (HSA) used ZnO, CuO, and ZnO:xCu (x = 0.1, 0.4, 1.0, 4.0, and 12.0) NCs. (3) Results: Substitutional incorporation of Cu2+ in the crystalline structure of ZnO and formation of nanocomposite were demonstrated by characterization. Graphite electrodes were used and the electrochemical signal increased by 40% when using ZnO:1Cu and 4Cu (0.25 mg·mL−1), in an immunosensor (0.372 mg·mL−1 of anti-alpha-amylase and 1% of casein). Different interactions of HSA with the alpha-amylase antibody were registered when adding the NCs together, either before or after the addition of saliva (4 μL). The immunosensor changed specificity due to the interaction of copper. The ZnO:1Cu and ZnO:4Cu samples showed 50% interference in detection when used before the addition of saliva. The immunosensor showed 100% specificity and a sensitivity of 0.00196 U·mL−1. (4) Conclusions: Results showed that the order of NCs addition in the sensors should be tested and evaluated to avoid misinterpretation in detection and to enable advances in the validation of the immunosensor.