Chromosomal and Genetic Variations

This study shows pancreatic tumors co-evolve with retrotransposons to modulate immune responses by regulating viral mimicry through SINEs and L1 retrotransposition.

The paper shows that distinct ORF1p coiled coil sequences from different L1 families can form entangled heterotrimers when co-expressed.

This study quantifies LINE-1 retrotransposition and expression in cancer, showing TP53 mutations enable retrotransposition by disinhibiting L1 expression and enabling reintegration.

The paper compares TG/CA repeats across sixteen primate genomes, finding higher numbers and expansion in humans compared to other primates.

This study presents a de novo genome assembly of Datura wrightii and identifies differentially expressed genes and the role of tandem duplications in herbivore defense.

The paper shows that the mitochondrial chromosome composition of Zostera marina remains stable across worldwide populations over 350,000 years despite individual variability.

The paper investigates genome organization in the neopolyploid flatworm Macrostomum lignano, revealing a unique rediploidization mechanism involving three subgenomes and heterozygosity maintenance through chromosomal rearrangements.

The paper shows that template-switching mutations generate over 6,000 hairpin structures in primates, leading to 18 new human miRNA genes, 26% of which emerged since primates originated.

The study examines meiotic behavior in tea plant pollen mother cells, identifying normal and abnormal phenomena including cytomixis and other meiotic errors.

This study presents a chromosome-level genome assembly of Gekko japonicus, identifying evolutionary mechanisms related to adaptive traits like climbing and detoxification.

The paper traces the origin and reactivation of a transposable element in a fungal wheat pathogen, showing its role in chromosomal rearrangements and loss of genomic control.

This study identifies a novel interaction between BmGtsf1L and BmVreteno's eTudor domain that facilitates piRNA biogenesis in Bombyx mori by connecting piRNA-loaded BmAgo3 and Gtsf1L.

This paper presents a high-quality, haplotype-resolved genome assembly of Malus fusca and identifies structural variants and a fire blight resistance locus.

The paper defines Lepidopteran Synteny Units (LSUs) to study macrosynteny conservation in butterflies and moths, finding it extends across >200 My and includes Trichoptera.

This paper assembles the genome of Sophora flavescens, revealing significant transposon and gene expansion, and characterizes gene expression and bioactive compound biosynthesis pathways.

The paper annotates lncRNA loci in Arabidopsis thaliana across multiple natural accessions, revealing high expression variability and silencing linked to transposable elements.

The paper investigates the genomic composition and regulatory networks of Coffea arabica sub-genomes, finding that essential gene expression machinery is preferentially located in one sub-genome.

The paper introduces DeepMEI, a deep learning tool for identifying mobile element insertions from whole-genome sequencing data, finding it outperforms existing methods and discovers more non-reference MEIs in 1000 Genome Project samples.

The paper examines how epigenomic divergence affects sequence polymorphism and the evolutionary fate of duplicate genes in Arabidopsis thaliana, finding that transcriptionally repressed genes accumulate more polymorphism and are more likely to pseudogenize.

The paper shows eccDNA-mediated transfer and evolution of herbicide resistance in pigweed hybrids.

The paper analyzes proteomic changes in Arabidopsis hybrids and allotetraploids, finding nonadditive protein expression and increased solubility of photosynthetic proteins associated with hybrid vigor.

This study presents a chromosome-scale genome assembly of Nicotiana tabacum, identifies genetic structure correlates, and builds a genotype-to-phenotype map for multiple traits using GenBank-scale data.

The paper presents a chromosome-level genome assembly of tree sparrow and identifies segmental duplications contributing to new gene formation and testis-biased expression.

The paper sequences and analyzes the mitochondrial genome of Microstegium vimineum to provide insights into its systematics, invasion history, and management.

The paper describes the creation and analysis of polyploid hybrids between Zea and Tripsacum species, examining chromosome inheritance and genome stability across generations.

The paper identifies novel Prdm9 alleles in wild mice and shows their association with fertility and sterility in hybrid males, supporting oligogenic control of hybrid sterility.

The paper detects structural variations and transposable element differences between lab strains of C. elegans, revealing significant genetic drift despite assumed isogenicity.

The paper identifies break-induced replication (BIR) as the primary recombination pathway in plant somatic hybrid mitochondria, supporting a model for mitochondrial horizontal gene transfer.

The paper improves the pearl millet genome assembly using Oxford Nanopore long reads and optical mapping, adding 200 Mb to the chromosome-level assembly and increasing gene completeness.

The paper identifies a novel MULE transposon in diatoms that mobilizes in real-time, inactivating the UMPS locus, and suggests a new mobilization mechanism with implications for genome evolution and biotechnology.