Chromosomal and Genetic Variations

This study evaluates TE polymorphic detection tools using simulated data based on real genomes, finding that few tools perform well and all are sensitive to genomic and TE characteristics.

The paper investigates how endogenous retroviruses in Drosophila have evolved to adapt their expression patterns and infectivity, leading to niche-specific diversification.

This study identifies transposon activities as key drivers of sweet orange cultivar selection and diversification over the last 500 years.

The paper analyzes piRNA expression variation across mouse strains and finds genetic differences contribute to strain-specific piRNA production, including from retrovirus insertions and protein-coding genes.

The paper measures nuclear genome size variation in Potamopyrgus antipodarum, finding higher genome content in sexual individuals and evidence for a recent whole-genome duplication.

The paper uses long-read genomics to study dikaryotic fungus genome biology, revealing nuclear-specific evolution and allele-specific expression.

The paper examines TE accumulation in Scalesia species and finds no significant variation despite hybridization and niche shifts, challenging the role of TEs in diversification.

The paper surveys Argonaute genes across 51 Caenorhabditis species, identifying gene gains, losses, and functional diversification, revealing dynamic evolution of small RNA pathways.

The paper analyzes subterminal heterochromatin in great apes, identifying its evolutionary origins and epigenetic features across chimpanzees, gorillas, and bonobos.

This study shows that homoeolog expression bias in hexaploid wheat is reprogrammed and stabilized within a few generations, varying based on parental lines.

This study constructs a chromosome-scale cannabis pangenome to explore genomic diversity and evolution, revealing low diversity in cannabinoid synthase genes and high diversity in other regions.

The paper identifies an endogenous retroviral element that uses an upstream enhancer for somatic expression and mobility in Drosophila intestine.

This study finds that reduced purifying selection and increased genetic drift in flies are associated with transposable element accumulation and larger genome sizes.

The paper identifies horizontal transfer of intron-containing transposons as a major source of new introns across eukaryotic lineages.

The paper examines genomic changes in 22 congeneric animal species pairs, finding varied synteny conservation patterns and no universal genomic change path during speciation.

The paper examines gene duplication and organization in C. elegans, finding weaker stage-specific expression patterns and more constrained duplicate gene expression compared to complex organisms.

This study introduces a method using LTR-RTs and SSM to assign subgenomes in polyploid genomes, applied to octoploid strawberry to identify three allopolyploidization events.

This paper describes the engineering of chromosome fission in maize using synthetic centromeres, resulting in stable, functional chromosome pairs that increase the diploid chromosome number from 20 to 22.

The paper examines how genomic composition in polyploid salamanders predicts physiological responses to temperature, finding a trade-off between water loss resistance and metabolic rate in hybrids.

The paper identifies 584 recent intron gain events in human genes by comparing human and vertebrate genomes and analyzing intronization mechanisms.

This paper presents a high-quality genome assembly of Annona squamosa and provides evolutionary insights into its demographic history and gene family expansions.

This study uses Fiber-seq to analyze TE regulatory potential in maize, revealing epigenetic patterns and gene interaction mechanisms.

The paper develops a high-throughput assay to test retrotransposon jumping activity and identifies variants that influence transposition.

The paper presents a chromosome-level genome assembly of Bostrychia moritziana, revealing genome size expansion and genetic adaptations in red algae.

This study shows that cancer-specific activation of retroelements disrupts gene function and tumour-promoting genes, with clinical and experimental evidence supporting these effects.

This study examines synapsis dynamics in Arabidopsis arenosa tetraploids, finding that improved synapsis efficiency correlates with meiotic stability and reduced crossover-related chromosome mispairing.

The paper investigates the molecular evolution of three reproductive barrier loci in maize and related species, identifying gene duplication, selection, and epigenetic silencing mechanisms.

The paper examines TE/host interactions in salamander genomes and finds no correlation between genome size and TE deletion rates or suppression, suggesting stochastic TE accumulation in gigantic genomes.

The paper updates the fungus gnat genome assembly using Hi-C data to produce chromosome-scale scaffolds, improving contig ordering, orientation, and chromosome assignment.