Biology subjects

de Oliveira, E. H. C.

Publications and source records attributed to de Oliveira, E. H. C..

3 recordsLinked to original sources

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2023

New parameters for the in vitro development of cell lines from fish species

The establishment of cell lines from fish species is becoming important because of the increase in interest of these cells for viral analysis, environmental monitoring and cytogenetic studies. However, there is some discussion about the best conditions for maintaining these cells. We describe here a protocol for primary cell lines which we have found to be reliable. Fin biopsies from two species, Geophagus proximus and Astyanax bimaculatus, were isolated and cultured. We used three culture media (Leibovitz-L15, Dulbecco s Modified Eagle Medium-DMEM and 199) with or without the addition of AmnioMax and a standard temperature of 29{o}C. The results showed that 199 medium was less efficient for both species. However, the cells of G. proximus had better proliferation in DMEM and L-15 media, while A. bimaculatus cells fared better in DMEM medium. The high concentration of L-glutamine and branched-chain amino acids (BCAAs) in the DMEM and L15 media was probably important for better adaptation of these cells. Furthermore, the addition of AmnioMax, a supplement rich in L-glutamine, increased cell proliferation in both species. Thus, the protocol initially established was tested in other tissues (fin, gills and kidney) of other fish species from the Amazon region. The cells were maintained in L-15 medium supplemented with 20% FBS (Fetal Bovine Serum) and 5% AmnioMax. It was observed that the cells were successfully subcultured and had a good proliferation, also the morphological characteristics were preserved. Thus, the methodology described in this research represents an innovative tool for the establishing of fish cell.

cell biology↗

bioRxiv2021

Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

The karyotype of most birds has remained considerably stable during more than 100 million years evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of three parrot genomes (monk parakeet, blue-fronted amazon, budgerigar), we uncovered frequent chromosome fusions and fissions among parrots, with most of them being lineage-specific. In particular, at least 12 chromosomes recurrently experienced inter-chromosomal fusions in different parrot lineages. Two conserved vertebrate genes, ALC1 and PARP3, with known functions in the repair of double-strand breaks and maintenance of genome stability, were specifically lost in parrots. The loss of ALC1 was associated with multiple deletions and an accumulation of CR1-psi, a novel subfamily of transposable elements (TEs) that recently amplified in parrots, while the loss of PARP3 was associated with an inversion. Additionally, the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. The newly formed neo-sex chromosomes were validated by our chromosomal painting, genomic and phylogenetic analyses. Transcriptome profiling for multiple tissues of males and females did not reveal signals of female-specific selection driving the formation of neo-sex chromosomes. Finally, we identified one W-specific satellite repeat that contributed to the unusual enlargement of the W chromosome in monk parakeet. Together, the combination of our genomic and cytogenetic analyses highlight the role of TEs and genetic drift in promoting chromosome rearrangements, gene loss and the evolution of neo-sex chromosome in parrots.

evolutionary biology↗