Chromosomal and Genetic Variations

Distinct genomic architectures but the same gene underlie the convergent evolution of a plant supergene

The paper identifies convergent evolution of a plant supergene through multiple genomic architectures, showing the same gene is duplicated and co-opted independently in different species.

Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects

The paper examines satellite DNA dynamics across multiple insect orders and ground beetle species, revealing significant variation in satDNA abundance and turnover across evolutionary scales.

Autopolyploid establishment under gametophytic self-incompatibility: the impact of self-fertilization and pollen limitation

This study investigates how selfing rates and pollen limitation affect tetraploid establishment under gametophytic self-incompatibility.

Centromeric origin of megabase-scale Arabidopsis interstitial telomeric repeat domains

The paper identifies centromeres as a source of telomeric sequences in Arabidopsis, showing ITR domains arise from centromeres through amplification and adopt a distinct chromatin state.

Karyotype evolution of angel insects (Zoraptera)

This study analyzes karyotype evolution in Zoraptera, refuting holocentric chromosomes and showing XY sex chromosomes are ancestral, while revealing genomic diversity despite morphological uniformity.

340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

The degree of subgenome expression bias in B. napus changes between cultivars, tissues and across time

This study examines subgenome expression bias in Brassica napus across cultivars, tissues, and developmental stages, finding that expression bias varies and depends on the metric used.

Independent evolutionary trajectories of genomic repeats and non-repeat genome features in Actinomycetota

The paper compares the evolutionary patterns of genomic repeats and non-repeat features in Actinomycetota, finding repeats are more labile and non-repeats show punctuated evolution.

Rapid chromosomal evolution and polycentromeric drive in sedges and rushes

The paper investigates chromosomal evolution in sedges and rushes, finding evidence of polycentromeres and their impact on genome rearrangement rates and segregation patterns.

Achiasmatic meiosis underlies propagation of clonal genome and B chromosomes in hexaploid Carassius gibelio females but not males

The paper shows that hexaploid Carassius gibelio females use achiasmatic meiosis to produce clonal eggs, while males have reduced fertility due to meiotic issues, and B chromosomes are stably inherited as univalents.

An extension of the Cx(Co)m model of crossover patterning to account for experimental mortality in Drosophila melanogaster

The paper extends a crossover model to account for experimental mortality in Drosophila melanogaster by incorporating binomial survival rates and marker-associated viability defects.

Two routes to land: Genomic underpinnings of parallel aerial egg deposition in aquatic Old-World Pila and New-World Pomacea (Ampullariidae)

This study identifies genomic and proteomic adaptations in two snail lineages that independently evolved aerial egg deposition, revealing convergent evolutionary mechanisms and horizontal gene transfer.

Exploring the Repetitive DNA Diversity in Solanum betaceum (Solanaceae)

This study characterizes repetitive DNA in Solanum betaceum, revealing its genomic composition and intraspecific variation across populations.

Biological implications of a detailed repeat annotation in Octopus vulgaris

The paper provides a refined repeat annotation of Octopus vulgaris genome, revealing higher repeat content and multiple TE expansion events compared to previous studies.

Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

Trichome and inflorescence evolution in the paleopolyploid tree genus Greyia Hook. & Harv.

This study presents chromosome-scale genomes for three Greyia species, revealing that regulatory divergence after a whole-genome triplication drives morphological variation in trichome and floral traits.

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and rare sex

This study examines genome evolution in parthenogenetic nematodes, revealing chromosome fusions, rearrangements, and evidence of rare sexual reproduction events.

Long-read sequencing reveals transposable element-derived chimeric transcripts at zygotic genome activation in mammalian embryos

This study uses long-read sequencing to identify chimeric transcripts from transposable elements in mouse and bovine embryos during zygotic genome activation, revealing species-specific patterns.

DupyliCate: mining, classifying, and characterizing gene duplications

DupyliCate is a Python tool for analyzing gene duplications across species, demonstrating its use on plant and microbial datasets.

Ancient persistence and recurrent emergence of structural variants across divergent Atlantic salmon lineages

The paper investigates the evolutionary origins of shared structural variants across Atlantic salmon lineages, finding they result from ancient persistence, recurrent mutation, and lineage-specific frequency changes.

Ecological opportunity and the onset of polyploid niche expansion waves

This paper shows that ecological drift and dispersal limitation, not adaptive advantages, can enable polyploid populations to establish and diverge from diploids, leading to niche divergence.

Genomic properties representing plant sex chromosome evolution interpreted with genome language models

The paper uses a genome language model to analyze plant Y chromosomes from Silene and Humulus, identifying shared genomic features and evolutionary patterns despite structural divergence.

Functional CENP-B boxes are selectively conserved at centromeric regions

The paper identifies that canonical CENP-B boxes are highly conserved in centromeres but not in ectopic sites, showing selective conservation and functional binding.

Convergent evolution through independent rearrangements in the primate amylase locus

The paper reconstructs the evolutionary history of amylase duplications in primates, showing convergent expression patterns and functional divergence across species.

Taxonomic context and genomic architecture jointly shape expression divergence across animals

The paper quantifies expression divergence rates and patterns across Drosophila and mammals, showing higher divergence in Drosophila and specific effects of nested gene architecture.

Pervasive co-option of prokaryotic adenine methyltransferases by eukaryotic retrotransposons

This study identifies eukaryotic retrotransposons that encode prokaryotic-like DNA adenine methyltransferases and shows their adaptation to host 6mA-associated chromatin.

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

ERVmancer is a phylogeny-informed method that resolves read-mapping ambiguity for HERVs, outperforming existing approaches and revealing new biology in breast cancer.

Quantifying the influence of genetic context on duplicated mammalian genes

This study quantifies how genetic context influences evolutionary rates in duplicated mammalian genes, finding that target copies in new genomic locations evolve faster than source copies.

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

This paper presents the first chromosome-scale, haplotype-resolved genome assembly and annotation for Carya glabra, revealing it as an autotetraploid and providing resources for ecological and agricultural studies.

Meiotic recombination spans almost entire chromosome arms in a fully monoarmed karyotype of an African annual killifish Nothobranchius virgatus

The paper analyzes meiotic recombination patterns in Nothobranchius virgatus, finding recombination spans nearly entire chromosome arms, excluding centromeres and telomeres.