comparative / phylogenetic analysis

The paper identifies dual lifestyle features of Tetraselmis spp. viruses by analyzing integrated viral elements in algal genomes and their transcriptional activity.

This study identifies oxidative DNA damage signatures in Leishmania donovani during sand fly infection, linking them to allelic and haplotype selection through genomic analysis.

The paper shows amino acids at protein termini evolve twice as fast as those in the center, due to weaker functional constraints, and highlights biases in selection inference methods.

This study finds that recent environmental stochasticity does not predict population resilience, showing instead that evolutionary history and phylogenetic relationships are more influential.

The paper examines developmental changes in opsin gene expression across ray-finned fishes, finding increased rod and long-wavelength sensitive cone opsin importance and decreased shorter wavelength sensitive cone opsin expression.

The paper shows that non-canonical shuffled ATG8 interacting motifs in C53 link UFMylation and autophagy, revealing an ancestral regulatory mechanism for ER homeostasis.

This study investigates how axon branching and asymmetry affect mitochondrial transport, mean age, and age density distributions in neurons using computational models.

This study reevaluates the evolution of troponin I and T in vertebrates, identifying new gene classes and genomic loci, and challenging the notion that TNNI3's N-terminal extension is unique to mammals.

This paper provides a revised phylogenetic classification of the genus Viola, incorporating phylogeny, morphology, chromosome counts, and ploidy data, and introduces new subgenera, sections, and subsections.

The paper shows marine annelids synthesize sitosterol, a phytosterol, challenging the assumption that phytosterol synthesis is exclusive to plants.

The paper uses an in-silico approach to analyze secretion system components in five Ralstonia solanacearum strains, identifying conserved and horizontally transferred systems.

This study investigates the evolutionary origins and loss of TCP genes, finding that the C6 gene arose through sequential domain gains and the C9 gene was lost in galliform birds.

This study identifies an expansion of oligopeptide transporter genes in rust fungi, suggesting a specialized role in nutrient acquisition during biotrophic growth.

This study compares the evolutionary rates of influenza A virus hemagglutinin H1 and H3 across different host species, finding higher nonsynonymous mutation rates in mammals and specific glycosylation site accumulation in humans and swine.

This study compares the transcriptional targets and interactomes of four coronavirus nsp1 proteins, revealing virus-specific effects on host gene expression and protein interactions.

This study compares genomes of orobanchaceous plants with different parasitic lifestyles to trace the evolutionary steps of plant parasitism.

This study conducts a phylogenetic meta-analysis and systematic review of coordination abilities across species to assess their evolutionary origins and data reliability.

The paper identifies candidate loci associated with adaptive traits in mustelids by analyzing genomic variation across species.

The paper identifies a novel composite translocon for polysaccharide export in Gram-negative bacteria, composed of EpsX and EpsY, and shows its widespread presence across species.

The paper compares laboratory-acquired mutations to the wild-type alleleome of E. coli, finding that lab mutations rarely exist in the wild-type alleleome and are less likely to be synonymous.

The paper investigates the emergence and clonal expansion of V. aestuarianus francensis lineages in Europe by analyzing genome sequences from environmental samples and showing evidence of selective bottlenecks and copper resistance islands.

This study identifies the S375F mutation in the Omicron spike protein as responsible for its reduced cleavage efficiency, fusogenicity, and rapid spread.

This study shows that genomic GC content variation in bacteria is influenced by ancient adaptation legacies, particularly through DNA replication and repair systems, rather than neutral processes.

This study compares metagenomic data from sponge microbiomes to identify novel biosynthetic gene clusters and their conservation across species.

The paper identifies evolutionary events leading to the gain and loss of a plant PRR's ability to recognize the HAMP In11 in legumes.

The paper identifies a mechanism called creative destruction that explains how new protein folds evolve from existing ones through gene duplication, merging, and adaptation.

The study identifies multiple alr genes in Hydractinia symbiolongicarpus that contribute to allorecognition, showing allelic variation and alternative splicing influence recognition phenotypes.

The paper examines how environmental factors influence gene expression and DNA methylation in Arabidopsis lyrata, revealing plasticity and genetic variation in response to lowland and alpine conditions.

The paper identifies amino acid residues determining FMRFamide activity at FaNaC channels and shows evolutionary conservation of ligand recognition determinants across DEG/ENaC channels.

The paper examines sulfur-mediated chalcogen and hydrogen bonds in proteins, showing their roles in stabilizing secondary structures and implications for protein design and drug discovery.