Chromosomal and Genetic Variations

This paper compares DNA shotgun read measurements and cytometric genome size estimates across species, finding discrepancies and highlighting the need for better measurement controls.

This study investigates the origins and adaptive consequences of polyploidy in the prairie grass Andropogon gerardi, finding that whole genome duplication is common and provides fitness advantages in xeric climates.

The paper shows that Ks histograms can reveal or obscure ancient whole genome duplications depending on evolutionary and demographic factors.

This study examines how thermal stress affects transposon regulation via small RNA pathways in male and female zebrafish germ cells, revealing sex-specific differences in genome defense mechanisms.

The paper presents a genome assembly for white sturgeon and identifies genetic markers for sex determination, aiding conservation and aquaculture efforts.

The paper shows that apoptosis releases non-coding DNA (ncDNA) containing horizontally transferred DNA-protein complexes from various species, revealing human evolutionary heritage in ncDNA.

The paper develops a short-read skim-seq method to identify apomictic genotypes in plants, finding 17 new apomictic genotypes in Malus species.

This study presents chromosome-level genome assemblies for Nicotiana attenuata and Nicotiana obtusifolia using long-read sequencing and Hi-C data, achieving high BUSCO completeness.

The paper investigates the genetic basis of twin and single spots in tobacco, finding that they arise primarily from deletions, translocations, and aneuploidy rather than homologous recombination.

The paper identifies pachytene piRNAs as precise gene regulators during meiosis, showing they target specific mRNAs through near-perfect complementarity.

The paper develops a germline enrichment method in Paramecium tetraurelia, revealing that germline-limited sequences contribute to somatic genome and transcriptome diversity through transposon remnants.

The paper identifies 648 recent transposable element horizontal transfers in Drosophila using 400 dipteran genomes, revealing patterns of transfer frequency and phylogenetic distance.

This study investigates the genomic basis of species richness disparity in Asteraceae by analyzing genome duplications and regulatory evolution.

The paper models interlocus gene conversion in tandem paralogues using Arabidopsis halleri HMA4 genes to show mosaic divergence patterns and the impact of IGC on gene copy diversity.

The paper identifies exon shuffling hotspots in Drosophila affinis genomes, showing they facilitate rapid gene creation and family formation through genomic sequence rearrangement.

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

This study generates chromosome-scale genome assemblies of germline restricted chromosomes (GRCs) in fungus gnats and finds they evolve dynamically with gene-rich content under strong purifying selection.

The paper identifies two Argonautes in Ascaris linked to programmed DNA elimination, showing their siRNAs target different genomic regions during chromosome remodeling.

The paper identifies programmed DNA elimination in three Caenorhabditis species, showing it was present in their last common ancestor and later lost in some lineages.

The paper investigates spatial genome organization during programmed DNA elimination in nematodes, showing conserved 3D genome reorganization across species.

This study compares mitogenomes of Rhopalocnemis phalloides and a congeneric species to investigate the origin and evolution of minicircular chromosomes, heteroplasmy, and conserved regions.

This study identifies transposable element insertions as a major cause of recessive lethality in Drosophila melanogaster, suggesting they drive lethal mutation frequencies through repeated invasions and suppression.

The paper generates high-quality genome assemblies for three Bouteloua species and identifies polyploidy and transposable elements, providing genomic resources for comparative studies.

The paper identifies TE fragments with regulatory potential in cerebellar development across species and introduces a framework to analyze their contribution to gene regulation.

The paper shows how the transposon Springer rewires gene expression and how Flamenco piRNA clusters remodel to allow transposon spread to the germline.

The paper presents chromosome-scale genome assemblies for two notothenioid fish species, providing insights into their evolutionary history and adaptation to climate change.

This study identifies SUGP1 as a key splicing factor in piRNA biogenesis in Bombyx mori, revealing its interaction with Y-box protein and dual role in piRNA maturation and transposon regulation.

The paper presents a high-quality genome assembly of Drosophila melanogaster ovarian somatic cells to study piRNA biology and transposon control.

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

This paper identifies chimeric pseudogenes formed by segmental duplications that exhibit functional roles in human-specific processes like genotoxic stress response and neuronal differentiation.