Chromosomal and Genetic Variations

Cytogenomic signatures of hybridisation in the genus Carpobrotus reveal biased parental dominance

The paper investigates hybridisation in Carpobrotus species, finding widespread introgression with a bias towards C. edulis and distinct cytogenomic signatures in hybrids.

Apomixis frequency in polyploid wild populations of Psidium cattleyanum f. lucidum (Myrteae, Myrtaceae)

This study examines apomixis frequency in polyploid populations of Psidium cattleyanum f. lucidum and finds pseudogamous apomixis is predominant, with ploidy levels influencing reproductive strategies and genetic structure.

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana

This study identifies 200,000 new transposable element insertions in Arabidopsis thaliana, revealing integration biases and adaptive potential of somatic transposition.

Copy Number Variation: A Substrate for Plant Adaptation and Stress Response in Arabidopsis

The paper identifies rapidly evolving gene families and environmentally associated CNVs in Arabidopsis species, showing their role in adaptation and stress response.

Ancestral gene flow shaped the singular origin of the Amazon molly

The paper investigates the origin of asexuality in the Amazon molly, showing that ancestral introgression between parental species contributed to its unique genomic makeup.

Higher-order Architecture Shapes Concerted Evolution in a Y-linked repeat array

The paper shows that the Su(Ste) Y-linked repeat array in Drosophila is organized into domains with conserved structure, which constrains gene conversion and copy-number dynamics.

Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

From junk to deleterious: Natural subtelomeric repeat amplifications impact fitness and cellular phenotypes in yeast

The paper shows that subtelomeric repeat amplifications in yeast reduce fitness and alter cellular phenotypes, moving repetitive DNA from neutral to deleterious.

Evolutionary genomics of host-transposon conflict, multilevel selection, and Red Queen dynamics

The paper tests the Red Queen dynamics hypothesis by analyzing TE distribution and host regulation in 78 teleost fish genomes, finding evidence of coevolutionary arms race.

Conserved Genic Composition Unravels Rapid Karyotype Evolution and Polyploidization across Plants

The paper introduces GouMang, a framework to trace karyotype evolution across plants, revealing conserved patterns and the role of whole-genome duplications in adaptation.

Evidence for post-allopolyploidy genetic exchanges between duplicated regions in three ancient polyploidies

The paper investigates late diploidization after three polyploidies by analyzing gene tree discordance using the POInT tool.

A conserved architectural domain shapes centromere evolution in Drosophila

The paper resolves centromere structure in Drosophila, showing conserved architectural domains despite DNA sequence variation.

Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis

The paper compares TE-rich and TE-poor duckweeds to show how TE amplification reshapes small RNA and DNA methylation landscapes, revealing species-specific epigenetic outcomes.

Regulatory logic and transposable element dynamics in nematode worm genomes

The paper models TE regulation in nematodes and finds that only outcrossing populations with parasitic TE regulation maintain TEs stably.

ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment

The paper identifies ChAHP as a repressor of SINE B2 elements by inhibiting TFIIIB recruitment, revealing a novel mechanism for controlling POL III-dependent transcription.

Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations

The paper analyzes the relationship between transposable elements (TEs) and histone marks across cell types, finding cell-type specific enrichments and associations with biological processes.

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction

The paper presents chromosome-scale genome assemblies of four duckweed species, revealing genomic plasticity and adaptations to aquatic environments through gene loss and pathway retention.

Evolutionary trajectories of teleost olfactory signaling genes shaped by long-term redundancy after whole-genome duplication

The paper traces the long-term functional evolution of duplicated olfactory marker protein genes after teleost-specific whole-genome duplication, showing extended redundancy and dosage-constrained divergence.

Gene regulatory divergence underlies tissue-specific and sex-specific misexpression in interspecies nematode hybrids

The paper investigates gene regulatory divergence in Caenorhabditis nematode hybrids, finding that cis-regulatory divergence disproportionately affects gene expression and contributes to sex-specific hybrid dysfunction.

Abundance, diversity and activity of endogenous retroviruses in the slow loris.

This study characterizes endogenous retroviruses in the slow loris, identifying active retroviral elements and their evolutionary dynamics across strepsirrhine primates.

Independent origins of fish endothermy converge on a developmental regulatory signature

The paper identifies a regulatory signature common to independent origins of endothermy in fish, showing convergent noncoding element acceleration near developmental genes.

Interspecies variation of 45S ribosomal DNA in vertebrates

This study analyzes interspecies variation in the 45S rDNA locus across vertebrates, revealing lineage-specific differences in organization, copy number, and sequence evolution.

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication

The paper corrects genome assemblies of two Lupinus species, revealing differential diploidization after a shared whole-genome duplication across six Lupinus species.

Haplotype-specific chromosome painting unveils recombination patterns in the holocentric species Rhynchospora breviuscula H.Pfeiff.

This study uses haplotype-specific chromosome painting to map meiotic recombination patterns in holocentric plants, revealing that recombination events are predominantly located in terminal chromosomal regions.

The evolution of structural variation across 500 million years of vertebrate evolution

This study identifies 35.3 million structural variants across vertebrates, showing significant variation in their abundance, mechanisms, and functional impact across species.

Processed pseudogenes as dynamic substrates of vertebrate genome evolution

The paper shows processed pseudogenes are dynamic evolutionary elements, not inert, and links their abundance to life-history traits and cancer-related dynamics across vertebrates.

Promoter Structural Variants are Drivers of Genome-Wide Differential Expression in Maize

The paper identifies promoter structural variants in maize that are associated with differential gene expression across tissues, often involving transposable elements.

Whole-genome duplication underlies conserved sexually biased expression of meiotic cohesin genes unique to the teleost fish lineage

The paper investigates the evolutionary and expression dynamics of meiotic cohesin genes in teleost fish, showing that whole-genome duplication and regulatory rewiring drive sex-biased expression patterns.

Mapping non-coding functional elements in allotetraploid Cyprinus carpio embryo development reveals subgenome variation of transcription regulation

The paper maps non-coding regulatory elements in common carp embryos, revealing subgenome-specific regulatory divergence during development.

Recurrent Duplication of the REST-NOA1 Locus Reveals a Hotspot of Regulatory Evolution Across Even-Toed Ungulates

The paper identifies recurrent duplication of the REST-NOA1 locus in ungulates and shows how structural divergence and regulatory changes contribute to immune system evolution.