Chromosomal and Genetic Variations

RetroSnake detects HERVs in NGS data using an end-to-end pipeline validated by wet-lab experiments, producing annotated insertions in an interactive HTML file.

The paper assembles and compares chromosome-level genomes of two Hyles hawkmoth species, revealing conserved synteny and chromosomal rearrangements.

The paper investigates TE-derived sRNA's potential role in gene regulation by analyzing Brachypodium distachyon's response to fungal infection.

The paper manually edits the B73 RefGen_v4 genome to close centromere gaps, adding sequence and improving centromere assemblies.

The paper investigates rDNA re-patterning in Lepidoptera, showing satellite arrays drive homology-mediated spread through extrachromosomal circles or ectopic recombination.

The paper develops a tool to genotype mobile element variants (MEVs) using short-read data and identifies population-specific MEs linked to disease and gene regulation.

The paper presents a chromosome-level assembly of the Cascade hop genome, identifies sex chromosomes, and reveals molecular evolution patterns in the Cannabaceae family.

The paper shows that SOX6 activates LINE-1 retrotransposons in PV+ interneurons, leading to increased morphological complexity through a novel CAPS2 isoform.

The paper determines the mitochondrial genome of Taichung 65 rice using a hybrid sequencing approach and classifies it as typical japonica.

The paper identifies satellite-free neocentromeres in zebras, showing centromere repositioning and Robertsonian fusions contribute to their formation.

This paper presents a chromosome-level genome of Dracaena cochinchinensis, identifies gene expansions linked to longevity and dragon's blood formation, and provides insights into its biological features.

The paper builds a TE atlas in pigs, showing young SINEs' roles in gene regulation, genetic diversity, and complex traits through multi-omics analysis.

The paper identifies three monotreme-specific reverse transcriptase-like genes derived from ERVs in platypus and echidna genomes, showing their conservation and testis-specific expression.

The paper develops a method to identify stress-associated genes in rice using DNA repeat probes and applies it to 9 Oryza species and other plants.

The paper shows that megabase-scale recombination landscapes in Arabidopsis are independent of sequence divergence and can be predicted by chromatin features.

This study completes the Triangle of U by sequencing the genome of Brassica carinata, revealing genomic features and gene family expansions linked to its agronomic traits.

The paper describes male pachytene karyotypes of 17 bird species using immunolocalization techniques, providing new data for three species, correcting data for ten, and confirming for four.

The paper identifies XRN-2 as an endoribonuclease involved in 5-end processing of precursor piRNAs in C. elegans, revealing its role in piRNA maturation and function.

The paper reports the somatic genome of Blepharisma stoltei, identifying a PiggyBac transposase homolog as a potential IES excisase, suggesting an evolutionary origin for genome editing.

The paper shows that Tf2 retrotransposons in fission yeast provide a fitness benefit by modulating the host's transcriptional response to metabolic stress.

The paper identifies 2500 putatively duplicated genes in Arabidopsis thaliana by analyzing SNP calls from short-read sequencing and validates them using de novo genome assemblies.

This study characterizes sex differences in recombination landscape in Rumex hastatulus, showing strong male-specific recombination suppression and its potential role in sex chromosome evolution.

The paper identifies maternally-deposited antisense piRNAs that silence transposons in zebrafish embryos by targeting young LTR retrotransposons and promoting H3K9me2/3 modification.

The paper analyzes 630 aquatic vertebrate genomes to create a compendium, revealing TE diversity and gene family evolution related to the water-to-land transition.

This study presents the genome of the camphor tree and shows how climate factors influence terpenoid biosynthesis gene expression and volatile compound accumulation.

This study sequenced and compared the genomes of two long-lived Ficus species to identify evolutionary mechanisms associated with their longevity.

The paper develops a predictive model of recombination rates in Arabidopsis thaliana by integrating epigenetic, genomic, and sequence divergence factors.

This study analyzes the evolutionary patterns of DDE transposons across eukaryotic hosts, finding host conservation, horizontal transfer, and trade-offs in host adaptation.

The paper develops a method to enrich and purify centromeric DNA from human cells, achieving 25-fold enrichment and up to 60% centromeric content in sequenced fractions.

piRNAdb is a database that catalogs piRNAs, their targets, and associated gene ontology terms, providing a user-friendly interface for piRNA research.