Chromosomal and Genetic Variations

This study examines gene expression and root mycobiome diversity in two allopolyploid orchids to understand how plasticity and environmental factors influence their ecological divergence and persistence.

The paper analyzes subtelomeric satellite DNA in Cannabaceae species to understand their evolutionary origins and chromosomal localization.

This paper highlights Boechera as a model for apomixis research, emphasizing its genetic diversity, reproductive mechanisms, and genomic adaptations that contribute to understanding asexual reproduction and its agricultural applications.

The paper presents the chromosome-scale assembly of the giant Pleurodeles waltl genome, revealing insights into its expansion and regeneration-related genes.

FishPi predicts piRNA-TE interactions in zebrafish, medaka, and tilapia by analyzing seed region complementarity and providing customizable outputs.

doubletrouble identifies and classifies gene and genome duplications across 822 eukaryotic genomes, offering tools for analysis and visualization.

The paper presents the reference genome of Cheirolophus tagananensis, providing tools for studying genetic adaptation and supporting conservation strategies.

The paper investigates the dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes, revealing expanded piwil1 genes and divergent piRNA-producing loci.

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

The paper investigates the role of transposable elements in the sex gap of longevity across three Drosophila species, finding age-related TE expression and Y chromosome effects on male lifespan.

The paper identifies sources of new miRNA gene emergence in Arabidopsis halleri, showing transposable elements contribute more than protein-coding genes.

This study shows p53 suppresses L1 retrotransposon-derived R-loops by recruiting repressive epigenetic marks and inhibiting activating marks, preventing DNA damage and inflammation.

The paper identifies Ohno-miRNAs, intragenic miRNA pairs from whole-genome duplication, and shows they have higher retention rates, sequence similarity, and regulate common targets compared to SSD miRNAs.

This study examines the evolutionary dynamics of the synaptonemal complex in Drosophila, revealing recurrent positive selection and diversification of SC genes through duplications and regulatory changes.

This study examines how whole-genome duplication affects genetic diversity and mutation load in Arabidopsis arenosa, showing increased diversity but modest load increases.

This study analyzes mitochondrial and chloroplast genomes of Arabidopsis thaliana to show that large repeats correlate with geography and phenotypes, and identify novel ORFs potentially from horizontal gene transfer.

This study compares manual and automated methods for transposable element annotation in Drosophila melanogaster and Aedes albopictus, finding that automated methods identify more TEs but manual curation provides more detailed classifications.

This study determines the parental origins of the allopolyploid Drosera anglica using genomic and transcriptomic data, finding it arose from D. linearis and D. rotundifolia.

The paper develops a stochastic model showing nonautonomous elements regulate autonomous elements' copy numbers and fluctuations, enabling their long-term coexistence and explaining evolutionary persistence.

The paper identifies ribosomal DNA arrays as the most H-DNA rich element in the human genome using the T2T assembly, showing 42.65-fold enrichment compared to chance.

CENdetectHOR identifies and analyzes HOR arrays in centromeres across species, revealing structural diversity and variations.

The paper identifies a new defense mechanism in Drosophila that enhances the piRNA pathway to control an expanded meiotic driver by increasing the expression of PIWI-clade nucleases.

This study identifies PRDM9's role in driving recombination hotspots in salmonids, showing rapid evolution and conservation of its function across vertebrates.

The paper shows insulin signaling represses R2 retrotransposon expression, which is necessary for rDNA copy number maintenance in Drosophila germline stem cells.

The paper presents a high-quality phased genome assembly of Urtica dioica using multiple sequencing technologies and a novel Hi-C protocol, revealing structural variation and gene content.

The paper identifies a novel endogenous retrovirus in slow lorises and suggests potential hybridization between species based on viral insertion similarities.

This study compares diploid and triploid apple varieties across 10 traits, finding triploids have higher phenolic content but overall phenotypic differences are subtle and often insignificant.

This study investigates the relationship between heterosporous reproduction and chromosome number reduction in green plants using phylo-transcriptomic analyses and gene family evolution models.

The paper investigates HTT and recombination in Saccharomyces Ty4 retrotransposons, finding multiple HTT events and novel clades formed through recombination.