Chromosomal and Genetic Variations

This paper introduces AGR, a pipeline to infer paleogenomes from modern species by using inter-species chromosomal synteny and hierarchical clustering.

This study identifies rapid chromosomal rearrangements and sex chromosome evolution in Pacific mackerels, linking them to reproductive isolation and speciation.

The paper identifies a segmental duplication-mediated deletion causing neocentromere formation in orangutans by analyzing structural and epigenetic variation.

This study examines transcriptomic changes in failing triploid seeds of Arabidopsis arenosa, identifying imprinted genes and revealing pathogen defense-like responses linked to the triploid block.

The paper shows that cytoplasmic inheritance of piRNAs is critical for piRNA biogenesis and that trans-acting piRNAs connect piRNA clusters into a functional network.

This paper presents haplotype-resolved genome assemblies for hybrid wheatgrass and its progenitor, revealing subgenome origins, expression bias, and reticulate evolution.

This study presents a high-quality genome assembly of Chaetoceros muelleri, revealing gene duplication, functional diversification, and TE-mediated genome plasticity.

This study characterizes piRNA expression dynamics across developmental stages in Blattella germanica ovaries, revealing coordinated fluctuations and a shift toward gene-derived piRNAs during vitellogeny.

The paper reconstructs ancestral recombination maps in placental mammals and finds that conserved low-recombination regions are under stronger purifying selection than conserved high-recombination regions.

The paper analyzes chromatin accessibility of maize knobs using DNS-seq data across four tissues, revealing tissue-specific dynamics in K180 knobs compared to TR-1 and centromeres.

The paper shows that infection with non-retroviral RNA viruses generates reverse-transcribed virus-derived DNA (vDNA) in multiple insect species and that this vDNA is secreted via extracellular vesicles.

LATTE quantifies TE expression across species and identifies TE-eQTLs, revealing distinct regulatory mechanisms and additional associations with complex traits.

This study reconstructs the genome and karyotype evolution of Sesamum and related species, revealing hybridization events and genetic changes linked to metabolic specialization.

The paper identifies SIRC ensembles in plant genomes, showing their ancient origin and phylogenetic signal, suggesting their utility in tracing evolutionary history and aiding genomic analysis.

The paper identifies Set1 as a key factor in Piwi-mediated transposon silencing and telomere control through piRNA biogenesis in Drosophila germline.

This study shows SUMO levels correlate with crossover rates across vertebrate species and within goat breeds, suggesting SUMO modulates meiotic crossover variation.

The paper evaluates how genome size and retrotransposon abundance correlate with gene family expansion in beetles using unified annotation frameworks.

This study identifies transposon-driven evolution of the MKK3 gene in barley, revealing three independent origins of nondormant alleles and their impact on seed dormancy.

The paper identifies a more accurate rDNA gene unit pattern in the human genome, characterized by (CTTT)n and (CT)n microsatellite aggregations ahead and behind the gene, respectively.

FuzzyClusTeR identifies and analyzes DNA repeat clusters, including both tandem and diffuse patterns, and demonstrates its application to telomeric-like repeats in human genomes.

ATHILAfinder detects ATHILA LTR retrotransposons in plant genomes with high accuracy, outperforming existing tools in recovery and precision.

The paper analyzes the genomic distribution of genes encoding secretion signals across eukaryotic genomes and finds they are enriched in regions with long flanking intergenic regions and specific repeat patterns.

This study investigates how trans-allelic epigenetic dominance in wild tomatoes disrupts hybrid endosperm development by causing genome-wide allelic imbalance.

The paper investigates the role of ancient whole-genome duplications in crop domestication by analyzing the enrichment of paleologs in domestication candidate genes across 22 species.

This study identifies Putzig's dual role in Piwi-mediated transposon silencing in Drosophila female germline by facilitating piRNA precursor transcription and co-transcriptional heterochromatin formation.

The paper examines ploidy variation in invasive Lantana camara populations in India, finding tetraploids dominate and no genetic differentiation among cytotypes.

TEgenomeSimulator generates synthetic genomes with configurable transposable element landscapes, offering greater flexibility and realism compared to existing simulators.

The paper shows that epigenetic mutants in Arabidopsis cause rDNA instabilities leading to changes in rRNA gene expression patterns through NOR conversions.

The paper develops a method to resolve collapsed chromosomal segments in polyploid Brachypodium genomes, improving assembly quality and capturing genomic architecture.

The paper identifies splicing deficiency in non-recombining mating-type chromosomes across phytoplankton species, showing how recombination suppression leads to transcript-level dysfunction.