Chromosomal and Genetic Variations

The paper introduces HERVarium, a database annotating human endogenous retroviral LTRs and their regulatory features, revealing structural and functional patterns across the genome.

The paper presents complete GRC assemblies from passerine birds, revealing their composition, evolution, and dynamic nature despite their stability in the avian karyotype.

The paper tests for positive selection in centromere-associated kinetochore proteins across diverse animal groups but finds sporadic positive selection in some proteins.

The paper identifies proto-point centromeres in Saccharomycodales yeast, showing they evolved from retrotransposon LTRs, supporting the hypothesis that point centromeres originated from ancestral retrotransposons.

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

The paper develops TiMEstamp to identify LINE-1 chimeric insertions in the human genome, revealing new chimeras and mechanisms like trans-splicing.

The paper analyzes higher-order repeat (HOR) structures in maize centromeres and knobs, finding they are widespread but not functionally specific to centromeres, while knobs show structured HOR patterns linked to meiotic drive.

The paper identifies extensive gene loss and a novel genetic instability called sequence stuttering on avian dot microchromosomes using long-read sequencing.

The paper compares T2T genomes of C. nigoni and C. briggsae, finding that self-fertilization is associated with loss of satellite DNA, particularly on the X chromosome.

The paper identifies transposable elements and repeat-induced point mutation as triggers of chromosomal instability and degeneration in a fungal pathogen through experimental progeny analysis.

The paper identifies 53 gene losses in squamates through chromosomal rearrangements and segmental deletions, highlighting their role in immune function and evolutionary adaptation.

The paper demonstrates somatic L1 retrotransposition in adult mouse liver using an intrahepatic reporter assay and identifies distinct regulatory mechanisms in tumor versus normal cells.

This paper presents a chromosome-level genome assembly of Urochloa humidicola, revealing its octoploid structure, evolutionary origins, and subgenome relationships.

The paper identifies Starships as vectors for horizontal transfer of transposable elements (TEs) in fungi, showing their role in TE bursts and genome structural changes.

This study links rapid termite diversification to increased transposable element activity across two evolutionary waves.

The paper shows piRNA specificity arises from tissue-specific modules acting on non-specific RNA sampling, with Yb guiding processing in somatic cells and catalytic Argonaute triggering amplification in germline cells.

panREPET identifies shared transposable elements across genomes to trace their dynamics, revealing TE bursts linked to climate events in Brachypodium distachyon.

The paper compares small RNA landscapes in two allopolyploid marsh orchid species and their diploid parents to understand how polyploidy affects genomic regulation.

The paper presents the first chromosome-level genome assembly of Flustra foliacea and identifies chromosomal fusions and retrotransposon enrichment in its genome.

The paper constructs a citrus super-pangenome from four ancestral species, revealing evolutionary patterns and genetic diversity through gene annotation, resequencing, and PAV analysis.

This study quantifies introgression's role in phylogenetic discordance among diploid Oryza species, finding it explains most gene tree-species tree conflict.

This study identifies ancient nuclear mitochondrial DNA segments in mammalian genomes using improved sequence comparison methods, revealing previously undetected NUMTs with origins over 100 million years ago.

The paper presents a chromosome-scale, haplotype-resolved genome assembly for Quercus virginiana, contributing to genomic resources for studying hybridization and structural genomic changes in oaks.

This study investigates interploidy admixture in Thymus sect. Mastichina using genomic data, revealing distinct diploid and tetraploid groups with complex genetic structuring and potential for cryptic diversity.

The paper identifies two types of piRNA clusters in planarians, Seed and Spread clusters, which balance piRNA diversity with off-target effect limitation through distinct mechanisms.

piRAT annotates, analyzes, and visualizes piRNAs from small RNA-seq data, providing reports and visualizations for cross-sample and cross-species studies.

This study examines how wheat domestication altered transposable element abundance and distribution, linking climate-driven genomic changes to key domestication traits.

The paper identifies two distinct Starship families in Pyricularia oryzae, showing differences in sequence evolution, epigenetic modifications, and impacts on genome variation and plant-fungal interactions.

The paper discovers three novel ancient whole genome duplications in Saccharomycotina yeasts, suggesting WGD may be more common in fungi than previously thought.