Chromosomal and Genetic Variations

The paper identifies multiple origins of autotetraploidy in Arabidopsis lyrata across Eurasia and shows how adaptive introgression stabilizes these polyploid forms.

The paper analyzes L1 retrotransposition in tumors using long-read sequencing, revealing synchronous L1 insertions drive chromosomal crossovers early in tumorigenesis.

This study shows that CCR4 maintains centromere epigenome and chromosome integrity in Arabidopsis by regulating RNA quality control and DNA methylation.

The paper shows that four Drosophila LTR-RTEs integrate into distinct chromatin domains and exhibit differential expression in specific tissues, leading to temporal and spatial niche partitioning.

The paper examines the evolutionary rates of nuclear and organellar genomes in land plants and finds they are positively linked, except in parasitic angiosperms.

The paper presents a chromosome-level genome assembly for the snowy owl and identifies evolutionary new centromeres seeded by a transposable element, showing lineage-specific centromere evolution.

The paper identifies ten novel endogenous retrovirus families in Anuran genomes, revealing recombined states and expanding the known evolutionary history of ERVs beyond mammals.

The paper shows that enhancing RNAi in testes via oocyte-specific Dicer does not rescue spermatogenic defects caused by Mili loss.

This paper presents a chromosome-level genome assembly of Dracaena cambodiana and compares it with Dracaena cochinchinesis to identify genetic features related to longevity and environmental adaptability.

regulaTER is an R library that predicts the regulatory roles of transposable elements using genomics data and validates its capabilities using EMT/MET transition data.

The paper presents a chromosome-level, haplotype-resolved genome of Eucalyptus regnans, revealing structural variations and haplotype-specific genes that may contribute to environmental adaptation.

The paper identifies chromosomal fusions and inversions in Arctic codfish genomes, showing their role in adaptation to cold environments and speciation.

This study presents a chromosome-level genome assembly of C. brenneri, revealing conserved intron number patterns and genome organization despite high genetic diversity.

The paper examines karyotype variation in Polyommatine butterflies, finding that the W sex chromosome remains intact despite chromosome fragmentation.

The paper presents a high-quality chromosome-level genome assembly of Mercurialis annua and evaluates its completeness and utility for evolutionary studies.

The paper identifies two St loci in Antirrhinum that suppress Tam3 transposition without affecting transposase production.

The paper presents a near complete genome assembly of the Oshima cherry, identifies centromeric regions, and compares them with related species to study genetic diversity and evolution.

The paper uses machine learning to classify plant LTR retrotransposons and identifies biologically relevant motifs through explainability analysis.

The paper validates TE insertions from RNAseq data in Drosophila brain transcriptomes and finds that only a minority of predicted insertions are confirmed by PCR, with gene expression differences observed in TE-containing genes.

The paper analyzes repeatome divergence in six hortensia species to trace Hydrangea evolution and domestication, identifying species-specific satellite DNAs as cytogenetic markers.

The paper identifies Overdrive as a gene essential for targeted sperm elimination in the Segregation Distorter system in Drosophila.

The paper presents a phased chromosome-level genome assembly of Amaranthus tuberculatus and identifies a sex-determining region with unique features and gene expression patterns.

The paper analyzes whole-genome polymorphism data from 27 Arabidopsis thaliana genomes to highlight challenges and insights in unbiased genetic variation characterization.

This paper presents a chromosome-level genome assembly of Uncaria rhynchophylla and identifies genes involved in (iso)rhynchophylline biosynthesis.

This study identifies thousands of chromosomal inversions in deer mice and shows that repeats, particularly centromeric satellite arrays, drive large-scale genomic rearrangements.

This study identifies B chromosomes in Atractylodes lancea and shows their non-Mendelian inheritance from female parents.

The paper compares piRNA sequence repertoires in two silkworm cell lines and finds that repertoire changeability negatively correlates with piRNA biogenesis efficiency due to competition between adjacent ping-pong sites.

This paper presents a chromosome-level genome assembly of Streptanthus diversifolius, revealing a recent whole genome duplication in the Thelypodieae tribe.

The paper analyzes repeat expression across the human lifespan in the neurotypical brain, identifying age-dependent upregulation of HERV-K in older adults.

FlaHMM automates the identification of piRNA clusters in Drosophila species using hidden Markov models and genome sequence data alone.