Chromosomal and Genetic Variations

The paper annotates conserved protein domains in human endogenous retroviruses using HMMER and InterProScan, revealing full-length retrovirus-like domains in multiple HERV families.

This paper presents a chromosome-scale genome assembly for Oxalis stricta, revealing its allotetraploid nature and synteny with related species.

This study compares the evolution of XY sex chromosomes in two closely related Asparagus clades, revealing distinct genetic mechanisms and timing for the origin of dioecy.

The paper provides genome size and ploidy level data for 1104 non-apomictic angiosperm species from the Eastern Alps using flow cytometry on silica-dried samples.

The paper tracks karyotype dynamics in Macrostomum lignano using flow cytometry, showing spontaneous de novo chromosome duplications in lab cultures and proposing a method to control karyotypes.

The paper examines telomeric repeat distribution in 41 Paphiopedilum species to understand chromosomal evolution and karyotype diversification, identifying patterns linked to structural processes like centric fission and subtelomeric rearrangement.

TEclass2 classifies transposable elements using a Transformer-based deep learning model, offering reliable results and a user-friendly tool for TE annotation.

This study presents a chromosome-scale genome assembly for Sarracenia purpurea and identifies genomic mechanisms underlying convergent evolution in carnivorous plants.

This study characterizes the evolutionary dynamics of mammalian microRNAs across 73 genomes, revealing conserved and lineage-specific patterns of miRNA family gains and losses.

This study identifies Squash as a cofactor of Spindle-E that ensures heterotypic ping-pong piRNA amplification in Drosophila ovaries, preventing transposable element de-repression.

This study identifies 28 candidate genes involved in B chromosome elimination in Sorghum purpureosericeum embryos through transcriptomic and genomic analysis.

The paper studies gene regulatory evolution in salmonids after autotetraploidization, finding that it is influenced by developmental and tissue-specific factors, with constraints at advanced embryogenesis.

The paper develops a framework to analyze multispecies synteny data and applies it to Rumex, finding accelerated syntenic evolution linked to transitions to dioecy and XY sex determination.

The paper identifies IAPEz-int elements as the source of virus-like particles in the mouse placenta and shows their trafficking across the maternal-fetal barrier.

The paper analyzes eQTL data in Atlantic salmon to show long-term dosage balance maintenance after a 100 million-year-old genome duplication.

The paper shows that the Drosophila Piwi-piRNA pathway silences transposons by degrading their RNA via the nuclear exosome, with TEsup proteins facilitating this process.

This study shows that acute heat shock rapidly disassembles and reassembles Drosophila piRNA cluster heterochromatin, with RDC re-localization independent of maternal piRNAs.

The paper provides the first direct evidence of transcription from germline-restricted chromosomes (GRCs) in fungus gnats, identifying expressed genes and a horizontally acquired bacterial region.

The paper compares transposon activity between polar bear subpopulations in different climate zones and links it to adaptation mechanisms.

The paper analyzes STR distribution across 117,253 organisms, finding significant taxonomic variation and higher STR abundance in eukaryotic and viral genomes compared to bacteria and archaea.

This study identifies a chimpanzee-specific retroviral insertion that influences gene regulation and brain development, highlighting its role in human-chimpanzee brain divergence.

The paper analyzes chromosomal evolution and polyploidy in 230 Andropogoneae species using phylogenomic methods, finding high chromosomal diversity and multiple evolutionary events.

The paper analyzes structural variants in three North American jay species using pangenome tools and long-read assemblies, revealing rapid genome evolution and population size effects on SV dynamics.

The paper presents a lineage-wide evolutionary analysis of 3D genome architecture and organization across brown algae, revealing conserved chromosomal features, lineage-specific rearrangements, and long-term co-evolution of centromeres and retrotransposons.

panHiTE detects population-specific transposable elements in large-scale plant genomes, improving sensitivity and precision while reducing redundancy and enabling TE-gene associations.

The paper analyzes the distribution of simple repeat lengths across mammalian genomes and shows that long repeats are abundant due to mutational dynamics, not natural selection.

The paper identifies a conserved cis-regulatory code across 589 grass species and finds that motif conservation declines rapidly but remains significant over evolutionary time, with adaptive changes linked to ecological transitions.

The paper examines centromere structure and location across nine yeast species, finding conserved chromosomal positions but diverse structures, suggesting in situ structural changes.

The paper investigates how natural genetic variation in Arabidopsis thaliana affects centromere-proximal crossover frequency and segregation distortion during meiosis.