Chromosomal and Genetic Variations

The paper identifies an excess of gene conversion and recombination events in gorillas linked to PRDM9 and Alu elements, showing lineage-specific motif targeting and depletion.

The paper identifies and analyzes mobile genetic elements in the gibbon genome, revealing their role in genome evolution and potential contributions to disease.

This study identifies a species-specific large-scale gene duplication in the European eel, suggesting a potential 4R WGD event, which may have facilitated its complex life cycle.

The paper presents the first de novo genome assembly of Nicotiana glauca and confirms the presence of a single cT-DNA insertion.

The paper introduces TagMap, a method for accurately mapping multiple transposable element insertions in complex genomes using modified tagmentation and PCR.

TruePaiR identifies complementary piRNA read pairs in sRNA sequencing data to assess piRNA amplification across species and tissues.

piClusterBusteR classifies and characterizes piRNA cluster loci across species, providing annotated and unannotated sequences for downstream analysis.

The paper identifies a bias towards 3n - 1 length tandem repeats in multiple eukaryotic genomes, suggesting a potential evolutionary and disease-related genomic phenomenon.

The paper analyzes the genome-wide impact of transposable elements on gene regulation, finding that Alu elements are associated with upregulated gene expression and contribute more to regulatory regions than ancient TEs.

The paper investigates genetic and epigenetic changes in hexaploid plants derived from a Brassica hybrid, finding more epigenetic than genetic variation in early generations.

The paper identifies chromosomal binding targets of SETMAR isoforms in colorectal cell lines and finds isoform-specific binding to Hsmar1 ends and non-conserved sites, with differing expression profiles between cell lines and tissues.

This study shows that TEX19.1 restricts L1 retrotransposon mobilisation in mouse embryonic stem cells by promoting the degradation of L1-ORF1p.

This study analyzes copy number variations (CNVs) in white spruce, finding they are mostly copy number losses, have high spontaneous mutation rates, and show transmission distortions affecting genetic variation.

The paper identifies an endogenous retrovirus insertion in C. elegans that contains the orphan gene F58H7.5, suggesting retroviral origins for this gene.

The paper improves a Bayesian method to analyze Alu element evolution, revealing fluctuating sequence constraints and over 4,000 replicative loci, challenging previous classifications.

The paper identifies DNA chimeras linked to tandem repeats and transposable elements in allotetraploid fish, showing their role in balancing sub-genomes and reducing genomic shock.

The paper analyzes polyploid fish hybrids to identify chimeric and mutated genes, finding high proportions in both tetraploid and triploid hybrids and linking some to phenotypic traits.