Chromosomal and Genetic Variations

Comparative chromosome-scale genomics of the ayahuasca liana Banisteriopsis caapi reveals paleopolyploid ancestry and recent tandem-gene expansions as candidate signatures of ethnovariety differentiation

The paper compares chromosome-scale genomes of two B. caapi ethnovarieties to identify genomic features associated with ethnovariety differentiation.

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Fragmented landscapes of mobile transposable element families bolster the diversity of large-effect alleles in Arabidopsis

The paper identifies over 200 new mobile transposable element families in Arabidopsis thaliana using pangenomic analysis, showing they contribute to large-effect alleles despite being rare in most strains.

Influence of the male germline on B chromosome transmission in D. melanogaster

This study investigates how male germline factors influence B chromosome transmission in D. melanogaster, finding that drag occurs without fertility defects or asymmetric segregation.

An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements

TE-Dee integrates TE knowledge, expression, and genetic associations to provide a structured resource for TE biology and AI model training.

Duplicate gene retention is partly repeatable across independent whole-genome duplications in plants, fungi and animals

The paper quantifies repeatable gene retention patterns across independent whole-genome duplications in plants, fungi, and animals, identifying gene-intrinsic factors influencing retention.

PanTEon: a cross-kingdom framework to guide the design of transposable element classifiers

PanTEon provides a cross-kingdom framework for reproducible TE classification, benchmarking machine learning methods and highlighting performance variations across TE superfamilies and lineages.

Living representatives of the spiralian ancestral karyotype revealed by two Lima genomes

The paper reports two Lima species with a 20-chromosome karyotype matching a proposed ancestral spiralian karyotype, revealing conserved synteny and lineage-specific fusions.

GLARE: Genomic Language model for Automated Repetitive Element classification

GLARE is a TE classifier that outperforms existing methods across multiple taxonomic groups and sequence quality conditions using a genomic language model fine-tuned on harmonized reference data.

Ayahuasca plant genomes reveal retrotransposon-derived centromeres and contrasting routes to DMT and β-carbolines

The paper presents the genomes of Ayahuasca source plants, revealing retrotransposon-derived centromeres and distinct biosynthetic pathways for DMT and beta-carbolines.

Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

Lasp family proteins generated by teleost-specific genome duplication

The paper examines the evolutionary fate of the nebulin superfamily after teleost-specific genome duplication in zebrafish and medaka, showing lineage-specific retention and expression divergence of duplicated LASP genes.

Origin and evolution of acrocentric chromosomes in human and great apes

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

Inverse relationship between mitochondrial and non-coding nuclear DNA content in free-living kinetoplastids

The paper investigates the relationship between mitochondrial and non-coding nuclear DNA content in kinetoplastids, finding an inverse correlation that suggests co-evolution of genome sizes.

Chromosome-scale genome assembly of the North American invasive Asteraceae, Tanacetum vulgare (common tansy)

This study assembles and annotates the genome of an invasive North American T. vulgare genotype using long-read sequencing, providing a reference for studying invasion biology and weed management.

The uplift of the Qinghai-Tibetan Plateau reshaped genome architecture and diversification of Asian torrent catfishes

This study shows how tectonic uplift influenced genome structure and diversification in Asian torrent catfishes through chromosomal rearrangements and evolutionary processes.

A 23-copy tandem repeat of a cytochrome P450 gene underlies an adaptive introgression breakthrough in Ciona intestinalis

The paper identifies a 23-copy tandem repeat of the CYP2U1c gene as the structural variant underlying adaptive introgression from C. robusta into C. intestinalis.

The role of methylation and structural variants in shaping the recombination landscape of barley

This study identifies genomic features that explain recombination variation in barley, showing methylation and structural variants jointly determine recombination hotspots and coldspots.

Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses

This study identifies germline-restricted chromosomes in birds as reservoirs for active retroviruses, showing their role in promoting transposition and speciation.

Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action

The paper analyzes polymorphic transposable elements in human pangenomes to reveal regulatory evolution mechanisms before fixation.

Breaking the species barrier: recurrent genomic introgressions from very distant lineages in a ciliate

This study shows that ciliates can break species barriers through recurrent horizontal gene transfer from highly divergent lineages, resulting in viable offspring.

Genomic structural variation in clownfish adaptive radiation

This study characterizes structural variation across 16 clownfish species, identifying extensive SVs and clarifying inversion events on chromosomes 18 and 9.

Population genetics of active transposable elements: overdispersion arises naturally from transposition-deletion-selection balance

The paper develops a stochastic model of transposable element dynamics showing overdispersion arises naturally from transposition-deletion-selection balance and validates it with Drosophila data.

Genome assembly of the C4 grass Themeda triandra confirms karyotype orthology with sorghum and reveals genetic variation across diverse environments

The paper assembles the genome of Themeda triandra, finds syntenic relationships with sorghum, and identifies genetic variation linked to environmental adaptation.

Functional specialization of TAF4b governs early prophase I entry and recombination frequency in Brassica rapa

This study identifies TAF4b's role in meiotic progression and recombination in Brassica rapa by analyzing mutant lines and transcriptomic data.

Dual-color fluorescent reporters resolve Alu and LINE-1 retrotransposition in single cells

The paper develops a fluorescent reporter to monitor Alu retrotransposition in single cells and shows it can also detect L1 retrotransposition and their co-occurrence.

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

The paper analyzes HERV-K(HML-2) structural variation and coding capacity across human pangenomes using long-read sequencing, revealing polymorphic loci and incomplete representation in reference genomes.

Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome

The paper identifies two PIF/Harbinger transposable element families in C. inopinata, showing differences in amplification timing and mobilisation competence.

Integration of the DD-genome reshapes gene transcription, chromatin architecture and metabolome of allohexaploid wheat leading to enhanced adaptability

This study investigates how integrating the DD genome into tetraploid wheat enhances its adaptability by altering gene transcription, chromatin structure, and metabolome.

A postmeiotic route to polyploidy

The paper identifies a novel mechanism for autopolyploidization in yeast called SEM, demonstrating triploid and tetraploid formation through postmeiotic endoreplication and mating.