Chromosomal and Genetic Variations

The paper shows that antisense transposon insertions into host genes trigger piRNA-mediated immunity in Drosophila by generating chimeric transcripts that initiate silencing.

The paper investigates how centromere divergence and allopolyploidy influence genome evolution in carnivorous sundews, revealing structural differences between species with distinct chromosomal architectures.

The paper profiles small and long RNA in human oocytes across stages, showing short-piRNAs broadly suppress transposons while long-piRNAs target specific ERVs.

The paper analyzes insertion sequences (ISs) in prokaryotic genomes using transposon ecology to uncover general principles and niche specificities shaping their distribution and activity.

This study uses genome and transcriptomic analyses of oat species to show that polyploidy creates functional redundancy, buffering mutations but hindering beneficial allele fixation, and proposes breeding strategies to overcome these challenges.

AlloSHP detects single homeologous polymorphisms in allopolyploids without genome assembly, enabling phylogenetic analysis of diploid-polyploid complexes.

The paper investigates how P-element insertions in the long non-coding RNA CR43651 affect piRNA-mediated silencing and fitness in Drosophila melanogaster.

This study investigates how ploidy and mating system affect genetic variance in Erysimum incanum, finding empirical results contradict theoretical predictions.

The paper identifies germline-restricted chromosomes (GRCs) in 6,700 passerine species, showing rapid evolution and functional gene retention despite programmed DNA elimination.

This study identifies ploidy-induced root anatomical changes in wheat that improved nutrient use efficiency and adaptation to Neolithic agroecosystems.

The paper analyzes ploidy levels in seeds of Psidium cattleyanum to determine the frequency of apomixis and sexuality and their implications for endosperm formation.

The paper identifies and characterizes functional and trans-dominant negative HERV-K (HML-2) Rec proteins, revealing their diverse regulatory roles in post-transcriptional processes.

The paper identifies a JAK2-HNRNPA1 pathway that represses retrotransposon activity in haematopoietic stem cells, reducing insertional mutagenesis.

The paper examines chromatin accessibility differences in hybrids of Drosophila species to explore how chromosomal rearrangements influence epigenetic divergence and reproductive isolation.

This study reveals that Mitrastemon yamamotoi has acquired over 60% of its mitochondrial DNA from its host through horizontal gene transfer, supporting the circle-mediated HGT model.

This study presents a chromosome-level genome assembly of Pinus massoniana Minlin WY36, revealing insights into conifer evolution and resin synthesis.

The paper identifies genomic changes in parthenogenetic Drosophila mercatorum, finding a 30-fold expansion of heterochromatin on Muller element F correlates with parthenogenetic ability.

The paper examines sex allocation differences between autotetraploid and diploid populations of Galax urceolata, finding increased pollen production in autotetraploids due to whole genome duplication.

This study shows male and female recombination rates in house mice evolve under distinct evolutionary programs, with males showing a unique adaptive optimum in their lineage.

VAMPIRE is a k-mer-based tool for TR discovery and analysis, revealing new insights into human and nonhuman primate centromeres and subtelomeres.

The paper presents chromosome-level genomes for two orchids, revealing insights into their evolutionary relationships and genome size variation.

The paper examines how genetic novelty contributes to early genomic differentiation in Drosophila yakuba mayottensis, showing that transposable elements drive rapid structural variant formation.

The paper identifies a new genus of endogenous pararetroviruses (EPRVs) with long terminal repeats (LTRs) in grasses, revealing their evolutionary history and integration patterns in barley and related species.

The paper identifies and maps RNAs associated with human centromeres using ChAR-seq in three cell lines, revealing three categories of centromere-bound RNAs.

PrinTE simulates genome evolution driven by transposable elements, revealing that genome size is strongly correlated with LTR retrotransposon dynamics and suggesting genome expansion followed by contraction in A. psidii.

The paper uses oligo-FISH to validate genome assemblies and produce the most precise karyotype for Lens species, confirming chromosome assignments and structural rearrangements.

This study defines the mutation spectrum in Arabidopsis thaliana centromeres, showing higher point mutation rates and homology-directed repair-driven indels.

This study identifies and characterizes piRNAs in the early embryo of Parhyale hawaiensis, showing their abundance early in development and subsequent reduction after germ cell specification.

This study investigates the mechanisms and timing of programmed DNA elimination in songbirds, identifying key cellular and epigenetic processes involved in the removal of the germline-restricted chromosome from somatic cells.

The paper investigates how biogeography influences transposable element (TE) composition in Drosophila melanogaster by analyzing HTT events across 285 drosophilid genomes.