Molecular and functional characterization of the Drosophila melanogaster conserved smORFome.

Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, and ∼182 are conserved in plants.

Genome-Wide Analysis of Cadmium-Induced, Germline Mutations in a Long-Term Mutation-Accumulation Experiment.

Background: Germline mutations provide the raw material for all evolutionary processes and contribute to the occurrence of spontaneous human diseases and disorders. Yet despite the daily interaction of humans and other organisms with an increasing number of chemicals that are potentially mutagenic, precise measurements of chemically induced changes to the genome-wide rate and spectrum of germline mutation are lacking.

Objectives: A large-scale mutation-accumulation experiment was propagated in the presence and absence of an environmentally relevant cadmium concentration to quantify the influence of cadmium on germline mutation rates and spectra.

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.

Background: A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level.

Genome-Wide Stress Responses to Copper and Arsenic in a Field Population of Daphnia.

Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level.

Copy number variation of a protease gene of Daphnia: Its role in population tolerance.

Copy number variation (CNV) of genes coding for certain enzymes has been shown to be responsible for adaptation of arthropods to anthropogenic toxins. Natural toxins produced by cyanobacteria in freshwater ecosystems, that is, protease inhibitors (PIs), have been demonstrated to increase in frequency over the last decades due to eutrophication and global warming. These PIs inhibit digestive proteases of Daphnia, the major herbivore of phytoplankton and cyanobacteria.

High mutational rates of large-scale duplication and deletion in Daphnia pulex.

Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D.

Hybridization and the Origin of Contagious Asexuality in Daphnia pulex.

Hybridization plays a potentially important role in the origin of obligate parthenogenesis (OP) in many organisms. However, it remains controversial whether hybridization directly triggers the transition from sexual reproduction to obligate asexuality or a hybrid genetic background enables asexual species to persist. Furthermore, we know little about the specific genetic elements from the divergent, yet still hybridizing lineages responsible for this transition and how these elements are further spread to create other OP lineages.

Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes.

Many organisms survive fluctuating and extreme environmental conditions by manifesting multiple distinct phenotypes during adulthood by means of developmental processes that enable phenotypic plasticity. We report on the discovery of putative plasticity-enabling genes that are involved in transforming the gill of the euryhaline teleost fish, Fundulus heteroclitus, from its freshwater to its seawater gill-type, a process that alters both morphology and function. Gene expression that normally enables osmotic plasticity is inhibited by arsenic.