Biology subjects

Villamayor, P. R.

Publications and source records attributed to Villamayor, P. R..

6 recordsLinked to original sources

bioRxiv2025

Retinoic acid production via the ray-finned fish gene beta-carotene oxygenase 1-like is essential for juvenile development

In vertebrates, vitamin A (VA) is crucial for development, tissue homeostasis, vision, and immunity. Retinal, a form of VA, is produced via enzymatic cleavage of {beta}-carotene by beta-carotene oxygenase 1 (bco1) and bco1-like (bco1l). While bco1 is found across vertebrate taxa, bco1l is a paralog of bco1 that we discover to have evolved in the ray-finned fishes, the most abundant, speciose, and commercially important group of fishes. We investigated the function of bco1l in ray-finned Siamese fighting fish, commonly known as betta, an emerging model for genetics and development. Using CRISPR-Cas9 knockouts, we find that lack of bco1l results in reduced VA and elevated {beta}-carotene in larvae, starting when animals have exhausted their yolk supply of retinal, followed by stunted growth and death during juvenile development. Exogenous retinoic acid rescues the mutation, demonstrating its deficiency causes these defects. bco1l is 4x more abundant than bco1 in the intestine. This, coupled with the inability of bco1 to sustain VA production in the bco1l mutant, indicates that bco1l is the primary enzyme for dietary carotenoid conversion into retinal. Our results show that VA production by bco1l is required for post-embryonic development, and that bco1l became essential after evolving via duplication of bco1.

genetics↗

bioRxiv2025

FULL-LENGTH HYBRID TRANSCRIPTOME OF THE OLFACTORY ROSETTE IN SENEGALESE SOLE (Solea senegalensis): AN ESSENTIAL GENOMIC RESOURCE TO IMPROVE REPRODUCTION AT FARMS

Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made over the past decade, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing technologies. A total of 20,670 transcripts actively expressed were identified: 13,941 were known transcripts, 5,758 were novel transcripts from known genes, and 971 were novel genes encoding novel transcripts. Special attention was paid to the olfactory receptor gene families (OlfC, OR, ORA and TAAR) expression. Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.

genomics↗

bioRxiv2024

Biostimulation methods based on chemical communication improve semen quality in male breeder rabbits.

Biostimulation aims to optimize reproductive parameters as part of animal management practices by modulating animal sensory systems. Chemical signals, mostly known as pheromones, have a great potential in this regard. This study was conducted to determine the influence of short-term male rabbit exposure to different biological secretions, potentially pheromone-mediated, on reproductive parameters of males. Four groups of 18 males each were exposed to A) doe urine, B) 2-phenoxyethanol, C) doe vaginal swab, and D) distilled water (control), three times over a 2.5h exposure window, just before semen collection. Semen volume, sperm concentration and motility, as well as subpopulation analysis of the spermatozoa were assessed for each condition. Additionally, testosterone levels in blood samples were monitored at five time points over the 2.5 h exposure window. We found a higher percentage of motile, progressive, fast progressive and mid-progressive spermatozoa in any of the three experimental groups compared to the control group. In contrast, the semen volume and the percentage of immotile and non-progressive spermatozoa was generally higher in the control group. We then identified a higher proportion of a subpopulation of fast and progressive spermatozoa in groups A, B, and C compared to group D. Our data indicates that sperm motility increases when animals are exposed to specific biological fluids potentially containing pheromones, and that an increase in sperm volume does not correlate with an increase in spermatozoa concentration, progressiveness, and speed. Finally, no differences in testosterone levels were found among comparisons, although males of groups A and C (exposed to natural female biological fluids) showed a tendency towards higher testosterone levels. In conclusion, our results indicate that rabbit sperm quality increases upon exposure to the biological secretions proposed, thereby supporting further investigation into their molecular identity. This exploration could eventually pave the way for implementing the use of pheromones in rabbit husbandry to enhance reproductive and productive parameters in farmed rabbits.

animal behavior and cognition↗

bioRxiv2024

A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula

The retina, whose basic cellular structure is highly conserved across vertebrates, constitutes an accessible system for studying the central nervous system. In recent years, single-cell RNA-sequencing studies have uncovered cellular diversity in the retina of a variety of species, providing new insights on retinal evolution and development. However, similar data in cartilaginous fishes, the sister group to all other extant jawed vertebrates, are still lacking. Here, we present a single-nucleus RNA-sequencing atlas of the postnatal retina of the catshark Scyliorhinus canicula, consisting of the expression profiles for 17,438 individual cells from three female, juvenile catshark specimens. Unsupervised clustering revealed 22 distinct cell types comprising all major retinal cell classes, as well as retinal progenitor cells (whose presence reflects the persistence of proliferative activity in postnatal stages in sharks) and oligodendrocytes. Thus, our dataset serves as a foundation for further studies on the development and function of the catshark retina. Moreover, integration of our atlas with data from other species will allow for a better understanding of vertebrate retinal evolution.

neuroscience↗

bioRxiv2023

Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

BackgroundSalmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. ResultsWe characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. ConclusionOur results highlight the key role of keratinocytes to coho salmons sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

genomics↗

bioRxiv2022

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor (fshr) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.

genomics↗