comparative / phylogenetic analysis

The paper identifies a resident bacterial community in the brains of healthy salmonids and shows its relationship to gut and blood microbiomes, with adaptations for brain colonization.

The paper develops a computational framework to simulate 5-ALA transport and fluorescence in glioblastoma patients, showing peak fluorescence occurs 2-7 hours post-administration, consistent with current guidelines.

The paper links fungal and bacterial functions in root-associated communities to root economics traits in a subtropical forest.

This study identifies a unique evolutionary pathway in Bartonella henselae for queuosine salvage, showing it can use both preQ1 and q, unlike other pathogens.

The paper uses phylogenetics and ancestral protein reconstruction to show that sodium-dependent substrate binding in glutamate transporters evolved before changes in coupling mechanisms.

The paper proposes a model where Xport-A stabilizes the first 5 transmembrane domains of Rhodopsin-1 during its biosynthesis, acting as a chaperone but not affecting the full-length protein.

This study investigates convergent evolution of desiccation tolerance in grasses, finding shared gene duplication and expression patterns alongside species-specific mechanisms.

The paper identifies distinct PE2 subcategories in paramyxoviruses and shows that four U-containing hexamer repeats are critical for filovirus genome replication.

The paper shows that the fungal gene ENB1, acquired from a bacterial operon, enables iron uptake in W/S clade yeasts and evolved through horizontal transfer and gene loss.

This study presents contiguous and complete assemblies of Blastocystis strains, revealing genetic and metabolic diversity linked to host ecology and horizontal gene transfer.

The paper identifies a transmembrane domain in septins from C. elegans and primates, showing it is required for membrane association and tissue integrity.

This study compares gene expression in Zymoseptoria tritici during susceptible, resistant, and non-host interactions to identify interaction-specific gene expression patterns and candidate effectors.

The paper reclassifies marine bacterial strains KMM 296 and related Cobetia species using genomic and chemotaxonomic data, suggesting they belong to a single species.

This study traces the emergence and spread of Streptococcus suis pathogens in pigs, linking their evolution to changes in farming practices and identifying genomic factors associated with pathogenicity.

The paper analyzes SR-B homologs across 165 eukaryotic species to show conserved beta barrel structure and lineage-specific sequence expansions in the CD36 apex region, suggesting evolutionary divergence in ligand sensing.

The paper examines the relationship between evolutionary age and range size in species, finding that age correlates with larger ranges but this effect is modulated by insularity and dispersal ability.

This study investigates winter mortality in freshwater mussels in northern Japan, finding high adult winter mortality and summer hypoxia as key factors limiting population growth.

This study identifies conserved amino acid residues and gene expression patterns that determine substrate preferences of FLS and DFR, showing gene expression exclusivity and evolutionary divergence in angiosperms.

This study identifies a mitochondrial carrier in Blastocystis that transports glycolytic intermediates, linking cytosolic and mitochondrial glycolysis and highlighting it as a potential drug target.

This study re-evaluates SARS-CoV-2 intrahost evolution rates in immunocompromised patients using multiple methods, finding no evidence of elevated rates compared to host-to-host transmission.

This study presents chromosome-level genome assemblies of two hemichordates to infer deuterostome ancestral chromosomal architecture and lineage-specific modifications.

This study compares hybrid male sterility in two rodent crosses, finding stage-dependent misexpression and sex-chromosome overexpression, suggesting distinct mechanisms in dwarf hamsters and house mice.

The paper shows MACPF proteins in sea anemones evolved from venomous to developmental functions through gene duplication and reverse-recruitment.

The paper examines sex-biased gene expression in Drosophila species with and without neo-sex chromosomes, finding more sex-biased genes in species with neo-sex chromosomes, suggesting a reduction in sexual conflict.

The paper identifies evolutionary shifts in lncRNA expression in the developing human cerebral cortex, showing increased de novo expression in excitatory neurons and associations with autism spectrum disorder.

The paper investigates the evolution of NRC immune receptor networks across plant lineages, finding significant expansion and complexity in lamiids compared to Ericales and campanulids.

This study links the rapid diversification of Boletales fungi to two climatic optima, showing their expansion coincided with warm-humid climates and host plant diversification.

The paper investigates the functional conservation of the NRC0 gene cluster across asterid plants and shows its role in immune responses.

This study examines the evolutionary dynamics of the synaptonemal complex in Drosophila, revealing recurrent positive selection and diversification of SC genes through duplications and regulatory changes.

The paper systematically screens fungal genomes to identify co-opted transposable element-derived domains, finding widespread TE contributions to protein function across the fungal kingdom.