Chromosomal and Genetic Variations

Transposable element-host genome evolutionary arms race revealed by multi-modal epigenomic profiling in a telomere-to-telomere human genome reference

The paper analyzes epigenomic data from twelve human cell lines to reveal how transposable elements evolve in response to host defense mechanisms across different chromatin states.

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

The paper presents chromosome-level genome assemblies for four Amaranthus species, revealing conserved sex chromosome inversions and providing resources for evolutionary and agronomic research.

Transposable element variation inferred from long-read sequences in wild house mice from temperate and tropical environments

This study identifies TE variation in wild house mice from temperate and tropical environments and finds some TE insertions associated with gene expression and positive selection.

Transposable elements drive phenotypic variation and shape the response to environmental changes in Drosophila melanogaster

This study shows that transposable elements (TEs) in Drosophila melanogaster cause phenotypic variation and affect responses to environmental changes.

Genomics and adaptive divergence of the allopolyploid grass Brachypodium hybridum in a pangenotypic framework

This study analyzes the origins and evolutionary dynamics of the allopolyploid grass Brachypodium hybridum using whole-genome sequencing and phylogenomic approaches, revealing three independent allopolyploidization events and subgenome-specific evolutionary patterns.

Subgenome-Level Phylogeny Reveals an Allopolyploid Origin of Chloranthales from Ancestral Monocot and Eudicot Lineages

The paper investigates the origin of Chloranthales by analyzing subgenome phylogenies and finds evidence of an ancient allopolyploidization event involving monocot and eudicot lineages.

First chromosome scale genome of Acrocomia aculeata

This paper presents the first chromosome-scale genome assembly of Acrocomia aculeata, providing insights for conservation genomics and plant breeding.

Evolutionary history and polyploidization lead to rapid shifts in chemodiversity of Hypericum

The paper investigates how polyploidization affects chemodiversity in Hypericum species, finding that higher ploidy levels correlate with increased metabolic diversity in some taxa.

Whole-genome duplication drives biosynthetic gene cluster fragmentation and regulatory rewiring of monoterpene indole alkaloid metabolism in Strychnos

This paper investigates how whole-genome duplication affects biosynthetic gene clusters in Strychnos species, showing that pathway function can persist despite fragmentation and regulatory rewiring.

Genome evolution at the extreme of angiosperm miniaturization

The paper examines genome evolution in duckweeds, showing that genome size and functional repertoire change independently during miniaturization, with transposable elements driving expansion and functional streamlining occurring through gene family contractions.

Synthetic genome expansion reveals a transcriptional constraint on genome size

This study expands the yeast genome with non-coding DNA and finds it reduces growth rate and endogenous mRNA concentration without affecting translation.

Nonredundant functions for Aedes albopictus Piwi5 in piRNA biogenesis and transposon silencing

This study shows that Piwi5 is essential for piRNA production and transposon silencing in Ae. albopictus, with loss of Piwi5 leading to increased transposon activity.

Expression of AAACTAC satellite repeats as a long noncoding RNA in the early oocyte of Drosophila virilis

The paper identifies a novel lncRNA, AAACTAC, expressed in early oocyte nuclei of Drosophila virilis and related species, suggesting a potential functional role in development.

The impact of P-Element-induced hybrid dysgenesis on the male germline in Drosophila simulans

This study investigates hybrid dysgenesis in male Drosophila simulans, showing elevated P-element transposition and gene expression changes, but less severe fertility defects compared to females.

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The paper sequenced genomes of Poaceae sister species to identify metabolic innovations that predate grass evolution, revealing gene duplications linked to starch and lignin biosynthesis.

TEstorm: a novel approach for activation and mobilization of LTR retrotransposons in plants using bioengineered viruses

TEstorm activates LTR retrotransposons in plants by temporarily silencing regulatory genes and inducing stress, leading to transposition and heritable genetic changes.

Topological mixing and irreversibility in animal chromosome evolution

The paper analyzes chromosomal evolution across 3,631 animal genomes to show that karyotype contraction and expansion drive genome evolution, with subchromosomal mixing and irreversibility shaping clade-specific trajectories.

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

This study compares TAD conservation and evolution across five cereal species, finding high conservation of TAD boundaries and their role in genome stability during evolution.

Ploidy-dependent modulation of DNA replication kinetics in Xenopus

The paper compares DNA replication kinetics across diploid, tetraploid, and dodecaploid Xenopus species, finding that higher ploidy does not always prolong S phase.

Robertsonian translocations in Danish sika deer (Cervus nippon). Markers for absent F1-hybridization with red deer (C. elaphus) and implications for selection, speciation and infertility

The paper analyzes chromosome numbers and Robertsonian translocations in Danish sika deer to assess hybridization with red deer and its implications for speciation and infertility.

Molecular arms race in WHO elements, a category of homing genetic elements distinct from inteins and introns

The paper identifies an evolutionary arms race between WHO endonucleases and their target site in the FBA1 gene in Torulaspora yeast, showing rapid sequence diversification to evade cleavage.

The chromosome-scale genome of the pine bark adelgid reveals conserved macrosynteny across Adelgidae

This paper presents the first chromosome-scale genome of Pineus strobi, revealing conserved macrosynteny across Adelgidae and supporting chromosome stability outside Aphididae.

A chromosome-level genome assembly of a "living fossil", the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

This paper presents the first chromosome-level genome assembly of Lepidurus arcticus, revealing genomic features and comparing it to a related species.

A Duplicate Resolved Paddlefish Genome Provides Insights into the Mechanisms of Rediploidisation and Hox Cluster Evolution

The paper analyzes a duplicate-resolved paddlefish genome to study rediploidisation and Hox cluster evolution, finding links between genome rearrangements, 3D architecture, and rediploidisation timing.

The multifunctional scaffold protein Small ovary couples piRNA-guided transposon recognition to nuclear RNA decay and heterochromatin formation

This paper identifies Sov as a scaffold protein linking piRNA recognition of transposon RNA to RNA decay and heterochromatin formation through distinct molecular mechanisms.

Non-coding DNA dictates cell size and impairs fitness by sequestering RNA polymerase

This study shows that non-coding DNA in yeast affects cell size and fitness by sequestering RNA polymerase, reducing transcript levels and impairing growth.

Lifestyles of Gypsy-family transposons shape their regulatory mechanisms

This study analyzes the evolutionary patterns of Gypsy-family LTR retrotransposons across 249 Drosophila genomes, revealing shifts in regulatory mechanisms and transcription factor involvement.

The piRNA pathway mediates transcriptional silencing of LTR retrotransposons in ovaries and somatic tissues of Aedes mosquitoes

This study shows that Piwi6 in Aedes mosquitoes suppresses LTR retrotransposons in both gonadal and somatic tissues by guiding H3K9me3 histone deposition.

Cytogenetic constraints on hybridization: A meta-analysis investigating the role of chromosome number in monocot hybrid evolution using a newly developed tool, the ploidy deviation index (PDI).

This study investigates how chromosome number divergence influences monocot hybrid evolution using a new metric, the Ploidy Deviation Index (PDI), finding homoploid hybrids are most common and challenging assumptions about polyploidy dominance.

Genomic and eco-geographic features of locally adapted inversions in wild sunflowers

This study identifies locally adaptive chromosomal inversions in wild sunflowers and finds they are more common in sympatric populations and have distinct genomic features.