Biology subjects

Cardoso, A. L.

Publications and source records attributed to Cardoso, A. L..

3 recordsLinked to original sources

bioRxiv2025

Genome Assembly of Astatotilapia latifasciata Uncovers B Chromosome Linked Chromatin Reorganization

B chromosomes (Bs) are supernumerary genomic elements found in many eukaryotes, yet their full sequence composition, functional potential, and regulatory impact on the host genome remain unclear. Here, we present a chromosome-level genome assembly of the cichlid fish Astatotilapia latifasciata, integrating PacBio long reads, Illumina short reads, and Hi-C chromatin contact maps to resolve both A and B chromosomes. The 0.93 Gb assembly (N50 = 36.2 Mb) includes a 34 Mb B chromosome containing 789 predicted protein-coding genes and a markedly higher density of transposable elements (TEs), especially long terminal repeats (LTR) retrotransposons. Transcriptome profiling revealed that B-linked genes are predominantly transcriptionally repressed relative to their A chromosome paralogs. Hi-C based chromatin modeling uncovered distinct 3D structural configurations associated with the B chromosome, including fewer topologically associating domains (TADs), reduced loop formation, and altered compartmentalization. These changes are linked to long-range chromatin interactions and genomic rearrangements, suggesting that the B chromosome reshapes the nuclear architecture of the host genome. Our study proposes a potential regulatory role of Bs in genome and provides a genomic resource for investigating chromosome evolution in cichlids.

genomics↗

bioRxiv2025

Adaptively integrated sequencing and assembly of near-complete genomes

Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. Cornetto is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).

genomics↗

bioRxiv2023

Universal conditions for establish continuous cell cultures in ray-finned fishes

Ray-finned fishes represent the most diverse vertebrate lineage and show extensive variations in physiology, ways of life and adaptations to marine and freshwater environments. Actinopterygii are largely exploited for human consumption and several species have been established as biological models. The in vitro culture of cells is fundamental for several fields of biological research, being an alternative for studies that use animals, since it mimics the cellular homogeneity of the original organisms beyond the advantage of reducing the variability of responses observed under in vivo conditions. In the case of fish cell cultures, besides being an important biomedical tool, they can offer important contributions to aquaculture and fish conservation. Hundreds of fish cell lines have been established using specific methods for each cell type and species. Here we describe an optimized protocol for obtaining cell cultures from the caudal fin of a wide range of ray-finned fishes including marine and freshwater species. The proliferative potential of these cultures makes them useful for several applications and the minimally invasive feature of this protocol makes it suitable for use in conservation plans.

cell biology↗