Chromosomal and Genetic Variations

The paper constructs fine-scale recombination maps in eleven plant species to analyze how gene structure and hotspot location influence recombination patterns.

This study re-evaluates the fusion hypothesis in Darevskia lizards, revealing premeiotic endoreplication as the mechanism for producing non-reduced eggs in obligate parthenogens.

RCPedia provides a comprehensive database of retrocopies across 44 species, offering genomic annotations, expression data, and query tools for genomic and evolutionary research.

The paper analyzes the contribution of transposable elements to regulatory elements in the human genome using ENCODE data, finding that ~25% of cCREs are TE-derived and show regulatory features similar to non-TE cCREs.

This study investigates the origins of near-identical antifreeze proteins in unrelated fish lineages, revealing distinct evolutionary pathways and mechanisms.

The paper shows that a meiotic driver in Drosophila pseudoobscura causes hybrid male sterility when moved between subspecies.

The paper presents a chromosome-scale genome assembly of Chia pinta and identifies population structure and interspecies introgression in Salvia species.

The paper investigates the evolutionary dynamics of genes involved in heterochromatin functions in Drosophila, finding they evolve faster than Polycomb-based repressive chromatin genes.

The paper identifies multiple origins of autotetraploidy in Arabidopsis lyrata across Eurasia and shows how adaptive introgression stabilizes these polyploid forms.

The paper analyzes L1 retrotransposition in tumors using long-read sequencing, revealing synchronous L1 insertions drive chromosomal crossovers early in tumorigenesis.

This study classifies LTR retrotransposons at the superfamily level using Predictive Bi-Clustering Trees, showing comparable performance to existing methods in D. melanogaster and A. thaliana.

This study presents high-quality genome assemblies and a gene family-based pangenome for two native North American apple species, providing resources for breeding and understanding their adaptation.

This study shows that CCR4 maintains centromere epigenome and chromosome integrity in Arabidopsis by regulating RNA quality control and DNA methylation.

This study shows that allopolyploidy in Commelina species enhances survival in urban environments compared to diploid relatives.

This study identifies a novel role for U7 snRNA in repressing HERV1/LTR12s and lincRNAs by inhibiting NF-Y transcription factor binding, suggesting a protective function in silencing genetic elements in specific cell types.

The paper shows that four Drosophila LTR-RTEs integrate into distinct chromatin domains and exhibit differential expression in specific tissues, leading to temporal and spatial niche partitioning.

The paper studies allopolyploidization in weeping willow, showing how sex chromosomes evolve and revert after hybridization between two dioecious species.

This study identifies ERV-DC8 as a replication-competent provirus in domestic cats that can infect human cells and is linked to FeLV-D.

CentIER identifies centromere regions in plant genomes using sequence specificity, achieving over 90% accuracy and providing insights into centromeric retrotransposons and tandem repeats in monocots and dicots.

The paper identifies Teosinte Pollen Drive, an RNAi-based gene drive in maize-teosinte hybrids, and shows its role in maize domestication and diversification through linked genetic elements.

The paper examines the evolutionary rates of nuclear and organellar genomes in land plants and finds they are positively linked, except in parasitic angiosperms.

The paper provides genome assemblies for three extant Kokia species, revealing genetic diversity and divergence patterns in the Hawaiian Islands endemic genus.

The paper develops a mechanistic model to explore how metabolic efficiency influences polyploid invasion and coexistence with diploid ancestors in plants.

This study identifies genetic adaptations to whole genome duplication in Cochlearia species, highlighting kinetochore and ion transport gene changes across multiple WGD events.

This paper analyzes homoeologous gene conversion and exchange in Gossypium allopolyploids using a new method and finds little evidence for gene conversion, with only one shared homoeologous exchange event identified.

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

The paper shows that the selfish element R2d2 in mice uses a hybrid mechanism in female meiosis to distort transmission by causing aneuploidy in the egg, leading to increased transmission of R2d2.

The paper introduces HELIANO, a tool for annotating Helitron-like elements in eukaryotic genomes, showing improved performance and identifying new elements across multiple species.

This study shows that ASY3 dosage affects crossover formation in Brassica napus, with reduced dosage increasing crossover numbers and disrupting interference.

The paper investigates how subgenome interactions affect growth diversity in intergeneric hybrid fish by analyzing whole-genome sequencing and mRNA-seq data.