Chromosomal and Genetic Variations

Sex-specific landscapes of crossover and non-crossover recombination in coppery titi monkeys (Plecturocebus cupreus)

This study estimates crossover and non-crossover recombination rates and patterns in coppery titi monkeys, finding sex-neutral rates but sex-specific genomic distributions of non-crossover events.

A highly contiguous genome assembly of Cyclamen persicum to accelerate functional genomics and breeding

This paper presents a high-quality genome assembly for Cyclamen persicum, enabling genomic studies and breeding improvements.

From tiny to massive: exploring genome evolution in the model 1 grass genus Brachypodium

This study presents chromosome-level assemblies of two perennial Brachypodium species, revealing genomic features like polyploidy and transposable element dynamics that shaped genome evolution.

Cross-ploidy hybridisation in Alpine woodrushes is associated with ecological additivity and scale-dependent niche divergence

This study examines cross-ploidy hybridisation in Alpine woodrushes, finding that ecological additivity holds at broader scales but niche divergence occurs at finer resolutions.

Bacterial DNA invasion triggers transposable element proliferation and genome expansion

The paper identifies a link between bacterial horizontal gene transfer and transposable element proliferation in nut weevils, contributing to genome expansion and molecular innovation.

Nowhere to Hide: The Effect of Centromere Architecture on LTR Retrotransposon Dynamics

This study tests a 'nowhere-to-hide' model linking centromere architecture to LTR retrotransposon dynamics, finding that holocentric chromosomes show different patterns of element persistence and removal compared to monocentric ones.

Genomic insights into the karyotypic radiation of a narrow endemic holocentric plant Carex helodes

The paper examines chromosomal rearrangements in Carex helodes, identifying genomic features associated with karyotypic evolution and environmental adaptation.

Evidence of two centromeres in the germline-restricted chromosome (GRC): insights from zebra finch lampbrush chromosomes

This study identifies two centromeres on the zebra finch GRC, suggesting a mechanism for its non-Mendelian inheritance through the maternal germline.

Chromosome-scale genome assembly of Cycas revoluta provides insights into cycad diversification and species diversity

The paper presents a chromosome-scale genome assembly of Cycas revoluta and identifies genes related to sex determination and thermogenesis, offering insights into cycad diversification.

Extensive mitogenome divergence across the Rafflesiaceae in size and impact of horizontal gene transfer

The paper compares mitochondrial genomes of Rafflesiaceae parasites and their host to show how horizontal gene transfer and structural changes lead to divergent mitogenome architectures.

Species-specific satellite DNA composition dictates PRC1-mediated pericentric heterochromatin

The paper shows that satellite DNA composition affects PRC1-mediated heterochromatin formation and mitotic spindle interactions in early embryos.

Explainable AI identifies recombination and chromatin environment as key predictors of subgenome evolution in maize and Brassica

The paper uses machine learning to identify recombination rate and chromatin environment as key factors influencing subgenome divergence in polyploid species like maize and Brassica.

Linking Germline Telomere Removal to Global Programmed DNA Elimination in Tetrahymena Genome Differentiation

The paper investigates the mechanism of telomere removal in Tetrahymena's germline micronucleus, showing it is part of a broader programmed DNA elimination process.

Evolutionary innovation through fusion of sequences from across the tree of life

The paper identifies 104 novel genes in arthropods formed by fusing horizontally transferred sequences with endogenous genes, showing they are expressed and under selection.

Near-Gapless and Haplotype-Resolved Capsella Genomes Enable Investigation into Genomic Consequences of Mating System Shifts

The paper presents high-quality genome assemblies and annotations for three Capsella species, revealing differences in transposable element dynamics and establishing a genomic database for future research.

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing

TEscape uses long-read sequencing to comprehensively annotate the human transposable element transcriptome, identifying over 83,000 previously unannotated isoforms.

Fertility Gene Introns Harbor Transposable Elements that Shape Y-Loop Architecture

The paper shows that transposable elements in Y-linked fertility genes of Drosophila are transcribed as part of nascent transcripts and contribute to Y-loop structure and male fertility.

Transcriptional Characterization of Nuclear-Integrated Organellar DNA in Populus

This study investigates the transcription of NUPTs and NUMTs in Populus using Oxford Nanopore DRS, revealing their transcriptional features and functional implications in gene regulation and genome evolution.

Comparative Analysis of Transposable Elements in Hermetia illucens

The paper compares transposable elements (TEs) across four Hermetia illucens genomes, finding lineage-specific TE family turnover and improved detection using a multi-genome repeat library.

Locus-Level Transposable Element Profiling Resolves Division-Coupled Transcriptional Dynamics During Human Endoderm Specification

The paper quantifies transposable element (TE) expression at both subfamily and locus levels during human endoderm differentiation, finding locus-level analysis reveals distinct transcriptional dynamics at cell division boundaries.

No evidence that polyploids arise during periods of environmental upheaval. A reply to Chen et al. (2026)

The paper challenges the claim that polyploidy in plants is linked to environmental upheaval by identifying methodological flaws in a previous study.

New genes play a prominent role in evolution of new sperm classes of Drosophila

The paper identifies new genes involved in the evolution of parasperm classes in Drosophila, showing their role in sperm divergence and altruistic traits.

Repetitive sequence material shapes the earliest stages of de novo gene evolution in insects

This study identifies de novo genes in crickets that arise from repetitive sequences, showing that such sequences are important in early gene evolution but not after gene establishment.

The immediate cellular response to whole-genome doubling is conserved across polyploid contexts

The paper compares the immediate cellular response to polyploidization across different contexts and finds conserved scaling of cell size and protein translation, with cell-cycle adaptations influencing outcomes.

A Lake Charr Pangenome Reveals Highly Conserved Ohnologs as Drivers of Phenotypic Diversity

The paper analyzes Lake Charr pangenome data to show conserved Ohnologs can drive adaptive evolution through structural variants and translocations.

Evolutionarily labile pachytene piRNAs target an altered set of mRNAs in male hybrids of house mouse subspecies

This study examines the evolutionary dynamics of pachytene piRNAs in mouse subspecies hybrids, showing that rapidly evolving piRNA genes can gain or lose mRNA targets in hybrids.

Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free centromere formation in Perissodactyla

The paper identifies satellite-free centromeres in Tapirus indicus and shows evolutionary hotspots for such centromeres in Perissodactyla, with uncoupling between CENP-A and CENP-B.

Recombination and repetitive genomic landscapes are decoupled in a close relative of Caenorhabditis elegans

The paper examines recombination rates and genomic features in C. inopinata, finding little covariation between recombination rates and repetitive element distribution.

EDTA v2: enabling scalable TE annotation in animal genomes

EDTA v2 improves transposable element annotation in animal genomes by adding LINE/SINE detection and enhancing scalability and speed.

Coexistence of piRNA and KZFP defense systems: Evolutionary dynamics of layered defense against transposable elements

The paper develops a mathematical model to analyze the evolutionary dynamics of piRNA and KZFP defense systems against transposable elements, showing how they can coexist through distinct suppression mechanisms.