Chromosomal and Genetic Variations

Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

A centromere but not just a centromere: structure and evolution of a selfish chromosomal supergene in monkeyflowers

The paper analyzes the structure and evolution of a selfish centromere in monkeyflowers, identifying genomic expansions and gene content differences that may contribute to meiotic drive.

Dissecting functional elements in giant genomes using the first generation of high quality salamander assemblies

The paper generates a high-quality axolotl genome assembly and identifies conserved non-coding elements linked to regeneration and cis-regulatory functions.

Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events

The paper analyzes allopolyploidization events in Brettanomyces bruxellensis using graph pangenomes to identify structural variants and their functional impacts.

A novel hybrid dysgenesis system in Drosophila melanogaster suggests that transposons may contribute to speciation

This study identifies a novel hybrid dysgenesis system in Drosophila melanogaster caused by Transib1, showing strong and temperature-tolerant effects, and demonstrates bidirectional gene flow barriers using two TEs.

Spatial expression evolution of duplicated genes post-whole genome duplication in cultivated tomato

This study examines how duplicated genes evolve spatial expression patterns after a genome triplication event in tomato, finding that ancestral expression states are often retained, with some experiencing expression gain or loss linked to fruit quality.

Shared genomic signatures of Arctic adaptation among distantly related plant lineages

The paper identifies shared genomic signatures of Arctic adaptation across distantly related plant species by comparing genome assemblies and analyzing selection pressures and repetitive elements.

Naturally arising de novo open reading frames as potential zinc chelators in Drosophila melanogaster

The paper identifies de novo open reading frames in Drosophila melanogaster that show sequence signatures indicative of metal-binding potential through bis-histidine motifs.

Hybrid Drosophila cell lines show selective genome instabilities

The paper establishes hybrid Drosophila cell lines to study genome instabilities and identifies incompatibility genes and chromosomal regions prone to loss in hybrids.

Conserved genes, discordant structure: a pangenomic view of plant mitochondrial genome evolution

This study analyzes over 300 plant mitochondrial genomes to show that gene content is conserved but structural complexity varies, driven by repeat proliferation and recombination rather than intergenomic DNA transfer.

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

This study presents a chromosome-scale genome assembly of Edelweiss, revealing its recent allotetraploid origin and localized subgenome dominance.

piRNA loss unleashes episodic transposition bursts

This study shows that loss of the piRNA pathway in Drosophila leads to episodic and stochastic transposition bursts, not just increased transposition rates.

From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

This paper presents a chromosome-scale genome assembly for rubber dandelion, identifies key rubber pathway genes, and links chromosome reorganization to domestication traits.

Chromosome-level Atlantic switchgrass assemblies reveal a supernumerary B-Chromosome with transcriptional and evolutionary impacts

The paper identifies a supernumerary B-Chromosome in Atlantic switchgrass, showing its evolutionary origin and impact on gene expression and genomic diversity.

Evidence for holocentric centromeres in the early branching apicomplexan parasite Cryptosporidium parvum

This study identifies diffuse centromere organization in Cryptosporidium parvum, distinct from regional centromeres in related apicomplexans, suggesting an independent evolutionary origin.

Gene-poor, repeat-rich Y chromosomes in two Neotropical malaria vectors, Anopheles cruzii and Anopheles aquasalis

The paper identifies Y-linked sequences in two Neotropical malaria vectors using YGS and CQ methods, revealing gene-poor, repeat-rich Y chromosomes with no intact protein-coding genes.

Differential k-mer distributions enable identification of tetrapod subterminal heterochromatin

The paper identifies subterminal heterochromatin in tetrapods using k-mer distributions, revealing ancient subgenome-specific repeats in Xenopus laevis.

Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants

This study examines evolutionary rate shifts in carnivorous plants to understand convergent and lineage-specific genomic adaptations.

Interaction of combined stressors and genetic background on recombination rate plasticity in Drosophila melanogaster

The paper examines how low temperature and hypoxia, alone and together, affect recombination rates in Drosophila melanogaster across different genetic backgrounds.

High-quality genome assembly of several Noccaea caerulescens accessions reveals gene expansion events associated with metal adaptation and hyperaccumulation

This study improves genome assemblies of Noccaea caerulescens accessions and identifies gene copy number variations linked to metal hyperaccumulation and adaptation.

Walking alone to the north: The origin and historical expansion of the polyploid parthenogenetic lineage in a weevil

The paper identifies a polyploid parthenogenetic lineage in a weevil that expanded northward, showing parallels with plant patterns of asexual reproduction and range expansion.

Unveiling the intraspecific genomic diversity of South American lowland maize landraces

This study examines genomic diversity in South American lowland maize landraces from Uruguay and Brazil, finding geographic patterns in genome size, heterochromatic knobs, and repetitive sequences.

Whole-genome alignment of 23 genomes reveals the tempo and genomic determinants of de novo gene birth in the Brassicaceae

The paper identifies 22,377 de novo genes in 21 Brassicaceae genomes, showing variation in birth/death rates and factors influencing their turnover.

Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci

The paper presents a chromosome-level genome of a type B avocado cultivar, identifies structural variations at flowering-type loci, and predicts the flowering type of a West Indian accession.

Synchronised developmental partitioning of visual opsins across parental subgenomes in allopolyploid Barbus barbus

The paper shows how duplicated opsin genes in the allopolyploid fish Barbus barbus are differentially expressed during development, with some switching between parental subgenomes and others remaining co-expressed.

Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression

The paper presents a near-complete genome assembly of the African turquoise killifish and evaluates how TR detection programs and TE workflows affect TE expression profiling.

All detectable ancient whole-genome duplications involve hybridization

The paper shows that ancient whole-genome duplications are often detected through hybridization rather than true polyploidy, based on Ks distribution analysis.

Chromosome-level genome assembly of Falcataria falcata provides insights into ancient polyploidy and duplicate gene evolution in Fabaceae

This study presents a chromosome-level genome assembly of Falcataria falcata to investigate ancient polyploidy and duplicate gene evolution in Fabaceae, finding evidence for both ancestral and lineage-specific WGD events.

Asymmetric inter-kingdom gene transfer and a horizontal transposon invasion in a powdery mildew fungus

The paper identifies recent horizontal DNA transfer events between plants and fungi, revealing asymmetric transfer patterns and dynamic evolutionary fates of transferred sequences.

First report on chromosome number and genome size of rare endemic birch Betula klokovii Zaverucha from Ukraine

This study reports the chromosome number and genome size of Betula klokovii, identifying a tetraploid cytotype and a potential triploid hybrid.