Chromosomal and Genetic Variations

Ischemia-reperfusion and acidosis induce retrotransposon derepression in the mouse brain

This study shows ischemia-reperfusion and acidosis increase retrotransposon expression in mouse brain tissue, suggesting a role in ischemic injury.

Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

The paper uses snRNA-seq to study B chromosome elimination in sorghum embryos, identifying two subpopulations of B-containing nuclei with distinct transcriptional profiles.

A transposon origin of large tandem repeats in the butterfly Papilio bianor

The paper identifies transposon-derived large tandem repeats in holocentric chromosomes of Papilio bianor and shows their role in chromosome structure and recombination.

TEExplorer: A Web Portal to Investigate TE-Epigenome Associations Across Human Cell Types

TEExplorer provides a web tool to explore TE-histone mark associations across human cell types using the EpiATLAS dataset and allows user data integration.

Disruption of small RNAs and mechanistic variation in Segregation Distorter, a sperm-killing drive system in Drosophila melanogaster

The paper investigates the role of Rsp-derived small RNAs in the Segregation Distorter drive system in Drosophila melanogaster, showing haplotype-specific variations in their contribution to drive strength.

Ancient transposable elements sustain global ecological adaptation despite chronically low nucleotide diversity

The paper shows ancient transposable element polymorphisms drive ecological adaptation in Spirodela polyrhiza despite low nucleotide diversity, challenging conventional models of adaptive potential.

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias

The paper presents a high-accuracy T2T rhesus macaque genome assembly, identifies subtelomeric repeats as a challenge, and reveals new genomic features and functional elements in these regions.

Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana.

This study shows that polymorphism increases recombination rates in Arabidopsis thaliana, shifting crossover hotspots to polymorphic regions and reducing them in non-polymorphic regions, driven by mismatch repair machinery.

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

The paper presents whole genome sequences of two elasmobranchs, analyzing genome size dynamics and genomic architecture, revealing correlations between chromosome size, repetitive elements, and gene duplication patterns.

A Complete Genome for the Common Marmoset

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.

Concerted evolution and unorthodox recombination of human subtelomeres

The paper analyzes subtelomeric regions across 465 human genomes to show widespread sequence exchange and recombination, revealing a population-scale pattern of concerted evolution.

Evolution of endogenized densoviral elements across aphid species

The paper studies the evolution of densoviral endogenous elements in aphids, finding lineage-specific variation and evidence for both vertical and horizontal transmission.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

The Polyploid History of Cultivated Dahlia

The paper assembles and annotates the genome of a tetraploid Dahlia variabilis cultivar, identifying it as a segmental tetraploid with evidence of auto- and allopolyploidy.

Genomic footprints of historical introgression between ancient lineages of wild Oryza AA-genome species with widely separated contemporary distributions

The paper identifies genomic footprints of historical introgression between geographically and phylogenetically distant Oryza AA-genome species.

Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function

The paper links structural variation to regulatory genome function in barley by analyzing epigenomic data across multiple genotypes and developmental contexts.

Animal retrozymes are nonautonomous sequences of Penelope-like elements

The paper investigates Non-LTR retrozymes across vertebrates, finding they are non-autonomous derivatives of Penelope-like elements and show distinct genomic distribution patterns.

Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides

The paper identifies genes and mechanisms involved in programmed chromosome elimination in Aegilops speltoides, focusing on B chromosome-encoded cohesin and centromere-related factors.

Recurrent evolution of cryptic triploids in cultivated enset increases yield

This paper identifies recurrent triploidy in cultivated enset, showing it increases yield and is selected by farmers.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Inter-haplotype inversions and repeat expansion in the sexually deceptive orchid Chiloglottis trapeziformis

This paper presents the first chromosome-scale, haplotype-resolved nuclear genome assembly for Chiloglottis trapeziformis, revealing structural variation and repeat-rich features.

CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis

This study uses CRISPR to reposition centromeres in Arabidopsis, showing how neo-chromosomes with altered centromere positions lead to meiotic segregation distortion and aneuploidy.

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

The paper presents a chromosome-level genome assembly of Cupressus sempervirens, revealing insights into conifer genome evolution and the role of transposable elements.

Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species

The paper constructs chromosome-scale genomes for three Cupressaceae species to study chromosomal evolution and speciation, finding chromosomal rearrangements and segmental duplications contributed to species divergence.

TIR-Learner v4: Accelerated annotation of terminal inverted repeat transposons

TIR-Learner v4 improves the speed and memory efficiency of TIR transposon annotation across large genomes.

Genome size, rather than sociality, predicts the turnover of duplicated genes in termites and hymenopterans

Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression

This study investigates chromosomal rearrangements in Carex laevigata, showing they arise in structurally fragile regions and contribute to genomic divergence through hybrid dysfunction and recombination suppression.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

The Dynamics of Long Terminal Repeat Proliferation in the Hesperis matronalis Genome

This study presents the genome sequence of Hesperis matronalis, revealing the dynamics of LTR retrotransposon proliferation and their role in genome expansion within the Brassicaceae family.

The contribution of non-additive genetic effects to the genetic variance of polyploid species.

This study investigates how genome doubling affects genetic variance in polyploid species, finding that genetic variance generally decreases, though non-additive effects can increase diversity in some cases.