comparative / phylogenetic analysis

Essential roles of HGT-derived sterol biosynthesis in trypanosomatid growth and parasitism

This study identifies HGT-derived genes critical for sterol biosynthesis in trypanosomatids, showing how gene loss and retention during parasitism shape metabolic adaptations.

Generalists link peaks in the shifting adaptive landscape of Australia's dragon lizards

The paper investigates the adaptive landscape of Australian dragon lizards, showing that generalist habitat use facilitated rapid morphological diversification after arrival in Australia.

Pangenome insights into structural variation and functional diversification of barley CCT motif genes

The paper analyzes CCT motif gene variation and functional diversification in barley using a pangenome and pan-transcriptome, revealing evolutionary dynamics and regulatory complexity.

Variation in genome architecture and epigenetic modification across the microsporidia phylogeny

This study compares genome and epigenetic architecture across multiple microsporidia clades, finding limited conservation and significant variation in genetic features and epigenetic modifications.

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture

The paper analyzes ICE content and variability in 1011 H. pylori strains, showing their prevalence, gene erosion, and role in shaping genome architecture through horizontal transfer and recombination.

Dyslipidemic SPTLC3 Integrates Bile Acid-FXR Signaling with Sphingolipid Remodeling in MASLD

This study identifies SPTLC3's role in integrating bile acid-FXR signaling with sphingolipid remodeling in MASLD, showing its dysregulation in human liver and association with disease.

Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion

The paper identifies genes associated with stromal resistance to placental and cancer invasion by comparing species and analyzing fibroblast responses.

Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates

This study investigates the evolution of saliva-related SCPP genes, identifying convergent duplications and positive selection in primates, with implications for adaptive diversification of saliva composition.

FliO is an evolutionarily conserved yet diversified core component of the bacterial flagellar type III secretion system

This study identifies FliO as a nearly ubiquitous and ancestral core component of the bacterial flagellar type III secretion system, showing structural diversity and functional repurposing across bacterial species.

Pangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae

The paper investigates genome evolution in pelagophyte algae, identifying lateral gene transfers contributing to pangenome diversity and ecological success.

Gene traffic mediated by transposable elements shaped the dynamic evolution of ancient sex chromosomes of varanid lizard

The paper investigates the evolution of sex chromosomes in varanid lizards, showing retrotransposons mediated gene recruitment and recombination suppression in the W chromosome.

Systems biology-enabled targeting of NF-κB and BCL2 overcomes microenvironment-mediated BH3-mimetic resistance in DLBCL.

This study identifies resistance mechanisms to BH3-mimetics in DLBCL and shows that combining BCL2 inhibition with non-canonical NF-κB inhibition overcomes microenvironment-mediated resistance.

Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders

The paper examines how the loss of a color morph in woodland salamanders affects asymmetric character release and evolutionary rates between morphs.

Comparative phylogenomics reveals multilevel genomic differentiation between annual and perennial Hordeum species

This study compares genomic differences between annual and perennial Hordeum species, finding recurrent patterns in gene expression, copy number, and co-expression related to growth and senescence.

Rescue of bacterial motility using two and three-species FliC chimeras

The paper engineers FliC chimeras from multiple bacterial species to restore motility in E. coli, finding that two chimeras containing the S. Typhimurium D2 domain successfully rescue motility.

Genomic rearrangements rewire chromatin contacts and drive adaptive gene expression divergence in mammals

Pervasive Horizontal Transfer of Adeno-Associated Virus Capsid Genes.

The paper reveals that AAV capsid genes have undergone extensive horizontal transfer across host species and rep lineages, with some variants originating from historical adenovirus stocks.

Comparative analysis of plasma and bone marrow nutrient levels in pediatric B-ALL patients

This study compares nutrient levels in plasma and bone marrow of pediatric B-ALL patients, identifying metabolic differences between subtypes and highlighting unique metabolic features in B-ALL circulation.

Evolution of the Jawed Vertebrate (Gnathostomata) Stomach through Gene Repertoire Loss: Findings from Agastric Species

The paper investigates gene loss in agastric vertebrates, finding no correlation between Gast and Grpr loss with the agastric phenotype and identifying retained gastric genes in echidnas.

The unique morphological basis and parallel evolutionary history of personate flowers in Penstemon

This study investigates the morphological basis and evolutionary history of personate flowers in Penstemon, finding distinct morphological mechanisms and multiple independent evolutionary origins.

Harnessing the Biosynthetic Diversity of Actinomycetes: Discovery of Unique Natural Products through Comparative Genomic and Metabolic Analysis

This paper develops a strategy combining genomic and metabolic analysis to discover novel natural products from actinomycetes, identifying two new peptides and their biosynthetic precursor.

Comparative genomic analysis reveals reduced pathogenicity of Ralstonia spp. in water

This study compares genomic data from Ralstonia spp. to show reduced pathogenicity in aquatic environments compared to plant and human-associated strains.

Optimal tuning not required: Birds communicate effectively with mismatched auditory filters.

This study shows that birds can communicate effectively despite mismatches between their auditory filters and vocalization frequencies, challenging the matched-filter hypothesis.

Comparative Genomics of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii Reveals Taxonomic Boundaries and Divergent Virulence Mechanisms

This study uses comparative genomics to analyze Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii, revealing shared genes, phylogenetic relationships, and differences in virulence mechanisms.

Comparative genomics-driven design of virus-delivered short RNA inserts triggering robust gene silencing

This study designs virus-delivered short RNA inserts (vsRNAi) for gene silencing in plants, showing effectiveness in Nicotiana benthamiana and crops like tomato and scarlet eggplant.

A human homolog of SIR2 antiphage proteins mediates immunity via the TLR pathway

The paper identifies SIRanc, a human homolog of bacterial antiphage SIR2 proteins, and shows it mediates innate immunity via the TLR pathway by degrading NAD+.

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

This study compares the genomics of seven Trichomonas species, revealing convergent genome size expansions in human-infecting lineages and genes involved in host-switching from birds to humans.

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism

This study compares the genomes of nematode-trapping fungi and non-NTF to identify genomic changes linked to carnivorism and adaptation to post-Permian-Triassic extinction environments.

Fate of a supergene in the shift from diploidy to polyploidy

This study examines the fate of a supergene in polyploid species by analyzing the genome of Primula grandis, finding degeneration of a key gene while other genes remain unaffected.

SEXUAL-DIMORPHISM IN VISUALLY GUIDED APPROACH BEHAVIOR EMERGES UNIQUELY DURING ADOLESCENCE

This study identifies sex-specific differences in visually guided approach behavior during adolescence in mice, showing female adolescents show enhanced approach to visual motion but less aggression compared to males.