Biology subjects

Fernandes, J. M. O.

Publications and source records attributed to Fernandes, J. M. O..

3 recordsLinked to original sources

bioRxiv2026

Rapid chromosomal rearrangements and sex chromosome turnover underlie the evolution of parapatric Pacific Scomber mackerels

Teleost display remarkable species diversity despite relatively conserved karyotypes, suggesting an important role for chromosomal rearrangements in speciation. Yet this hypothesis remains poorly tested in pelagic marine fishes, as genomic studies have predominantly focused on freshwater and coastal taxa. In this study, we investigated the genomic basis of hybrid incompatibility between two parapatric Pacific mackerels, Scomber japonicus and S. australasicus, hypothesizing chromosomal rearrangements as the major driving forces. We generated haplotype-resolved de novo genome assemblies for both Pacific species and assessed genomic rearrangements along with the genome of the Atlantic species, S. scombrus, reconstructed from publicly available data. Comparative genomic analyses revealed extensive chromosomal rearrangements across the genomes. Notably, the rate of chromosomal inversions was approximately sevenfold higher between the two Pacific species than between allopatric lineages. These rearrangements included complex structural changes involving megabase-scale inversions and associated translocations. Our analyses also showed that the sex chromosomes of the three species evolved independently. In the two Pacific species, large recombination-suppression regions (>10 Mb) arose convergently but through distinct mechanisms: tandem chromosomal inversions in S. japonicus and, most likely, transposable element-mediated sequence divergence in S. australasicus. By contrast, recombination suppression in S. scombrus is restricted to a [~]14 kb hemizygous region containing amhr2Y, generated by duplication and translocation. Population-level analyses further revealed ongoing evolution of recombination-suppressed regions in the Pacific species and uncovered multiple Y chromosome lineages in S. australasicus that differ markedly in the extent of recombination suppression. Together, these results demonstrate rapid structural genome evolution in Scomber and provide a genomic framework for understanding how chromosomal rearrangements contribute to reproductive isolation, sex chromosome turnover, and the diversification of pelagic marine fishes.

evolutionary biology↗

bioRxiv2024

Altered spawning seasons of Atlantic salmon broodstock genetically and epigenetically influence cell cycle and lipid-mediated regulations in their offspring

Manipulating spawning seasons of Atlantic salmon (Salmo salar) is a common practice to facilitate year-round harvesting in salmon aquaculture. This process involves adjusting water temperature and light regime to control female broodstock maturation. However, recent studies have indicated that altered spawning seasons can significantly affect the nutritional status and growth performance of the offspring. Therefore, gaining a deeper understanding of the biological regulations influenced by these alterations is crucial to enhance the growth performance of fish over multiple generations. In this study, we investigated omics data from four different spawning seasons achieved through recirculating aquaculture systems (RAS) and sea-pen-based approaches. In addition to the normal spawning season in November (sea-pen), three altered seasons were designated: off-season (five-month advance, RAS), early season (two-month advance, sea-pen), and late season (two-month delay, sea-pen). We conducted comprehensive gene expression and DNA methylation analysis on liver samples collected from the start-feeding larvae of the next generation. Our results revealed distinct gene expression and DNA methylation patterns associated with the altered spawning seasons. Specifically, offspring from RAS-based off-season exhibited altered lipid-mediated regulation, while those from sea-pen-based early and late seasons showed changes in cellular processes, particularly in cell cycle regulation when compared to the normal season. The consequences of our findings are significant for growth and health, potentially providing information for developing valuable tools for assessing growth potential and optimizing production strategies in aquaculture. Author SummaryThis study examines the impact of manipulating Atlantic salmon spawning seasons in aquaculture on genetic and epigenetic regulations in their offspring. Manipulating water temperature and light cycles during broodstock rearing allows for year-round harvesting. In aquaculture, altering spawning seasons is a common practice; however, recent research suggests that these changes affect the nutritional status and growth of offspring. To understand these effects at the molecular level, we analysed transcriptomic and epigenetic data from salmon offspring born to broodstock with four different spawning seasons. Our results reveal distinct transcriptomic and epigenetic patterns associated with altered seasons, influencing lipid metabolism and cell cycle regulation. These findings hold significant implications for improving aquaculture practices, potentially enhancing growth performance and nutritional quality of farmed salmon across generations as temperature and light are crucial abiotic factors influencing the next generation. Furthermore, our study potentially contributes to understanding the impact of climate change on the spawning behaviour of aquatic vertebrates, particularly in relation to increasing global ocean temperatures and the resulting changes in photoperiod as species migrate northward in the Northern Hemisphere, experiencing longer daylight in summer and shorter daylight in winter.

genomics↗

bioRxiv2022

CircPrime: a web-based platform for design of specific circular RNA primers

BackgroundCircular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. The tenth of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. ResultsHere, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. ConclusionsUser-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database (NCBI).

bioinformatics↗