Chromosomal and Genetic Variations

The paper shows that RNAi targets noncoding regions of VANDAL TEs, while VANC proteins evolved to escape this silencing, suggesting a co-evolutionary arms race between TEs and host defense mechanisms.

The paper reports the genome of a homosporous lycophyte, revealing that LTR-RTs drive genome size expansion through a birth-death mode unique to homosporous species.

The paper studies the evolution of G2/Jockey-3, a retroelement associated with centromeres in Drosophila melanogaster, finding it is likely a selfish element that targets centromeres to evade host defenses.

The paper identifies structural variants and H3K4me3 domains in two closely related fish species, showing their role in cis-regulatory divergence and phenotypic traits like metabolism and immunity.

The paper examines transcriptomic responses in synthetic allohexaploid wheat and finds minimal gene expression changes, primarily on the D subgenome, with no significant TE-gene associations.

The paper presents chromosome-scale genome assemblies for five Brassica oleracea morphotypes and analyzes their structural variations and evolutionary dynamics.

The paper presents the genome of Chinese fir, revealing evolutionary insights into gymnosperms and seed plant origins through phylogenomic and genomic analyses.

The paper examines the unique TE landscape in deer mice, showing LTR retrotransposons dominate over LINEs due to ERV invasion and KZNF gene expansion.

The paper studies dicentric chromosome breakage in Drosophila melanogaster and finds that breakage hotspots are not conserved and are influenced by pericentric heterochromatin and centromere origin.

The paper creates a homology guide for six Oncorhynchus salmon species to analyze duplicate retention and rediploidization patterns after a whole genome duplication event, finding retained duplicates are more adaptive.

The paper identifies LTR5_Hs viral proteins and virus-like particles in hPGCLCs, showing their activation during early germ cell development and suppression upon gonadal anlagen settlement.

The paper presents a chromosome-scale genome of the Mongolian gerbil with sequenced centromeres, revealing new insights into centromere structure and heterochromatin distribution.

The paper uses long-read RNA sequencing to study TE-gene transcripts in Arabidopsis, finding epigenetic regulation of their production and impact on gene function.

The paper presents a bioinformatics pipeline to assess evolutionary relationships among Drosophila species using class II transposon analysis and finds close relationships between D. melanogaster and other Drosophilidae species.

This study shows that synthetic mouse L1 retrotransposition efficiency is due to sequence changes and a 3UTR deletion, not just ORF GC content, and highlights the need to reconsider synthetic L1 constructs.

This study reactivates an errantivirus in Drosophila somatic cells, showing it can invade oocytes and trigger a germline immune response.

This study analyzes HSAT1 satellite DNA, showing its transcription in human cells and identifying size-varying polyadenylated transcripts.

This study examines numtogenesis patterns across 16 mouse strains by aligning nuclear and mitochondrial genomes, revealing strain-specific differences and phylogenetic relationships.

The paper identifies a DNA repair strategy in C. elegans somatic cells that significantly increases transposon mobilization rates compared to germline cells.

The paper identifies widespread horizontal gene transfer events in eukaryotic genomes across multiple species and shows their impact on genome evolution.

TrEMOLO estimates transposable element allele frequencies using long-read sequencing data by combining assembly and mapping approaches, outperforming existing tools in benchmark tests.

The paper identifies recent transposable element bursts in Zymoseptoria tritici genomes triggered by insertions near genes and GC-rich niches, revealing how genomic features influence TE proliferation.

This study compares piRNA sequences, targets, and functions in C. briggsae and C. elegans, revealing conserved genomic organization and divergent small RNA amplification patterns.

The paper investigates how selfish toxin-antidote elements evade silencing in C. tropicalis by showing maternal mRNA licenses zygotic expression through counteracting piRNAs.

The paper identifies that C. elegans piRNAs preferentially bind to coding regions of mRNAs, leading to secondary silencing small RNAs, and shows CSR-1 inhibits this process through two mechanisms.

The paper investigates strain-level variation in CENP-A association with centromeres in mice, finding strain-specific differences that challenge the idea that centromere function depends solely on satellite array size.

The paper analyzes IESs in Blepharisma stoltei, revealing MITEs as a major source of IESs and challenging current models of transposon domestication in ciliates.

The paper investigates TE activity and its potential impact on gene expression in response to statin treatment using computational tools.

This study identifies human-specific HERV LTR regulatory insertions linked to genes involved in development, fertility, and neurological disorders, revealing their broad phenotypic impacts.

The paper characterizes structural variation in Heliconius butterfly genomes and links it to chromatin accessibility and cis-regulatory elements.