whole-genome sequencing

The MarR-family regulator TilR links biosynthesis of enterotoxin tilimycin with physiologic adaptation in Klebsiella oxytoca

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

Genomic signatures of positive selection and relaxed selective constraints associated with convergent dietary specialisation

The paper identifies genomic signatures of positive selection and relaxed constraints in Dysdera spiders with convergent dietary specialisation on woodlice.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

Temporal changes in genetic variation during the invasion of Lygodium japonicum in North America

This study uses herbarium specimens to analyze genetic variation in Lygodium japonicum during its invasion of North America, identifying Asia as the source and finding evidence of rapid adaptation and reduced non-coding diversity.

Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

The paper assesses genetic load and structural variation in American black bear populations, finding elevated levels in an isolated population.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

Genomic signatures distinguish isolates of Salmonella Typhimurium from humans and livestock

The paper distinguishes human and livestock-associated Salmonella Typhimurium isolates using genomic signatures and machine learning.

Do divergent mitochondrial backgrounds alter the fate of nuclear alleles during hybridization and admixture?

The paper tests if mitochondrial backgrounds influence nuclear allele fate during hybridization, finding no evidence of such effects despite expected incompatibilities.

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Creation of genomic chimeras via megabase scale genome expansion

This paper introduces ACE, a method to create genomic chimeras by integrating large genomic segments from donor cells into a recipient genome, demonstrating its ability to generate stable chimeric organisms across species barriers.

Tools for genetic mapping and gene identification in Caenorhabditis briggsae

The paper updates a toolkit for genetic studies in C. briggsae by identifying indel variants and mapping mutations to genes using high-throughput sequencing.

Widespread Saccharomyces hybridization in agave fermentations arises repeatedly from asymmetric parental diversity

The paper identifies widespread Saccharomyces hybridization in agave fermentations, showing multiple independent origins and asymmetric parental genetic diversity.

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

The paper investigates correlations between molecular and morphological evolutionary rates across eukaryotes and finds little evidence of a link, suggesting differing evolutionary dynamics at genomic and phenotypic levels.

How mutation rate evolves: Gene expression shapes genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans

The paper investigates how gene expression influences genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans, finding that highly expressed genes have lower mutation rates due to transcription-coupled repair.

Lineage-specific histories rather than shared drivers shape olfactory evolution in New World monkeys

The paper investigates olfactory receptor repertoire variation in New World monkeys, finding that lineage-specific histories, not shared ecological drivers, shape olfactory evolution.

Structural Variant Aware Identity-by-Descent Detection on Pangenome Graphs

GIBD detects IBD segments in pangenome graphs and annotates them with structural variants, outperforming existing methods in accuracy and speed.

Genomic analysis of the Streptococcus anginosus group; taxonomic implications, evolutionary insights and clinical considerations

This study uses genomic analysis to reclassify the Streptococcus anginosus group into four taxa, revealing diversity and lineage-associated traits linked to invasive disease.

Somatic structural variation discovery on cancer pangenome graphs

JANUS discovers somatic structural variants in cancer genomes using a pangenome graph approach, achieving high accuracy and efficiency compared to traditional methods.

Toward space-optimal approximate colored indexes at scale

This paper introduces Zindex, a space-efficient indexing framework for large-scale sequence repositories, achieving compact storage and fast query performance with novel interleaved filters and merging mechanisms.

Contrasting Range and Demographic Histories in two Palearctic Dragonfly Species (Odonata: Anisoptera)

This study examines the relationship between climatic suitability and effective population size in two dragonfly species, finding they are not directly correlated.

Theoretical prediction of assembly contiguity

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

Genome-wide Analysis of the VQ Gene Family and Expression Profiling in Sorghum bicolor

This study identifies and characterizes VQ genes in sorghum, showing their differential expression and potential roles in salt stress tolerance.

Genomic features and instability of linezolid resistance in vancomycin-resistant Enterococcus faecalis ST525

This study examines genomic features and resistance mechanisms in vancomycin-resistant Enterococcus faecalis ST525 isolates, revealing variable linezolid resistance despite a single mutational mechanism.

Measuring satellite arrays of the human Y chromosome from sequencing reads

The paper introduces Yruler, a tool to measure Y chromosome satellite arrays from sequencing reads without alignment, revealing lineage-specific variations in satellite length and composition.

Genomic evidence of a single domestication origin for modern cattle

The paper uses whole-genome analyses to challenge the two-domestication model of cattle, showing zebu originated from admixture between taurine cattle and Indian aurochs with introgression from gaur-like or banteng-like populations.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

Phenotypic and Molecular Characterization of Potentially New Shigella boydii Serotype in Bangladesh

The paper characterizes a unique cluster of Shigella-like organisms in Bangladesh, identifying them as potentially a new serotype of S. boydii based on phenotypic, genotypic, and serological analyses.

Short-read whole-genome sequencing identifies the Tg(Tal1-cre/ERT)42-056Jrg transgene insertion site on mouse chromosome 4