Biology subjects

Nery, M. F.

Publications and source records attributed to Nery, M. F..

3 recordsLinked to original sources

bioRxiv2025

The small ORFeome of Tribolium castaneum reveals deeply conserved small ORFs broadly expressed across tissues

Small open reading frames (small ORFs/smORFs/sORFs) were historically overlooked due to their short length (<100 codons) and detection challenges. It is widely accepted that small ORFs are rarely conserved across distant taxa, particularly in deeply rooted ancestors. Growing evidence supports their biological relevance and potential roles in gene innovation. Here, we integrated genomic, transcriptomic, and proteomic datasets to identify and characterize 454 putative small ORFs in Tribolium castaneum. Conservation analyses revealed 230 small ORFs conserved within Coleoptera, 167 in insects, 85 in arthropods, 39 in eukaryotes, and six in bacteria. Conserved small ORFs displayed higher GC content ([~]44.87%), with bacterial-conserved sequences exceeding 50%. Functional enrichment revealed dozens of small ORFs associated with catalytic, transporter, structural, and regulatory roles. Binding site predictions indicated 254 small ORFs possess protein-protein interaction potential. Expression profiles across 14 RNA-seq libraries spanning multiple developmental stages showed 40.1% of small ORFs expressed (TPM >1) in at least one sample, and 16.5% expressed in five or more libraries. Conserved small ORFs showed broader and more stable expression, while lineage-specific ones displayed restricted expression, mostly in gonads or embryos. Isoformic and small CDSs were the most widely expressed classes. Notably, 29 small ORFs exhibited transcriptional and translational support (Swiss-Prot and/or Ribo-seq), 28 being small CDSs. A total of 390 small ORFs had potential paralogs, supporting gene duplication as a mechanism for small ORF emergence. Altogether, our findings reinforce that small ORFs, contrary to initial assumptions, can be deeply conserved and potentially perform key roles in evolutionary processes.

genomics↗

bioRxiv2022

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of non-collinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared to other reptiles, and harbor a higher genetic load compared to green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage. Statement of significanceSea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application.

genomics↗

bioRxiv2021

Positive selection in multiple salivary gland proteins of Anophelinae reveals potential targets for vector control

Anopheles is a genus belonging to the Culicidae family, which has great medical importance due to its role as a vector of Plasmodium, the parasite responsible for malaria. From Anopheles functional genomics, great focus has been given to the salivary gland proteins (SGPs) group. This class of proteins is essential to blood-feeding behavior as they have attributes such as vasodilators and anti-clotting properties. Recently, a comprehensive review on Anopheles SGPs was performed, however the authors did not deeply explore the adaptive molecular evolution of these genes. In this context, this work aimed to perform a more detailed analysis of the adaptive molecular evolution of SGPs in Anopheles, carrying out positive selection and gene families evolution analysis on 824 SGPs. Our results show that most SGPs have positively selected sites that can be used as targets in the development of new strategies for vector control. Notably, we were not able to find any evidence of an accelerated shift in the copy-number variation of SGPs compared with other proteins, as suggested in previous works. Significance StatementSalivary gland proteins (SGPs) are essential to blood-feeding behavior in Anopheles and they are the most studied class of proteins in blood-feeding insects. However a proper molecular evolution analysis on SGPs in Anopheles is missing. In our analyses we observed that most SGPs have positively selected sites and we were not able to find any evidence of an accelerated shift in the copy-number of SGPs compared with other proteins, as stated in the literature. Our results can open new venues in the development of new strategies for vector control.

evolutionary biology↗