Chromosomal and Genetic Variations

The paper develops a simple piRNA cluster annotation method for non-model insects, validated on mosquito genomes.

This study uses a multi-ancestry GWAS to identify genetic loci associated with variation in LINE-1 and Alu insertion numbers, highlighting potential regulatory mechanisms and disease links.

The paper characterizes and compares the repeatome of two Cenchrus species to identify subgenome-specific markers.

The paper analyzes centromere structure and function in stick insects, revealing a functionally monocentric system with holocentric-like features and chromosome-specific centromeres.

The paper investigates the effect of a truncated LINE1 sequence (t1519) on gene expression, finding it suppresses expression in long protein-coding genes and certain lncRNA genes.

TRACK is a pipeline for identifying and comparing tandem repeats across species, offering tools for cataloging, filtering, and population genetic analysis.

The paper compares genome fractionation patterns in maize and its wild relatives, finding distinct subgenome retention and gene loss trends between species.

This study presents the first collection of sex-specific recombination maps across 40 fish species, revealing links between recombination rates, karyotype, and sex-specific crossover positioning.

This study identifies natural heat resilience factors in Arabidopsis thaliana that enhance meiotic stability under heat stress, with implications for crop breeding.

This paper presents a chromosome-scale genome assembly for the polyploid, amphicarpic plant Cardamine chenopodiifolia using long-read sequencing.

This study identifies pangenomic structural variant patterns in Brassica napus, revealing evolutionary diversification across morphotypes and ecotypes through whole-genome long-read sequencing.

The paper uses exome sequencing of Danio species to show zebrafish has an ancient hybrid origin and recent gene flow, with genomic regions supporting different evolutionary relationships.

The paper analyzes horizontal transfer of transposable elements in 247 animal species, finding that phylogenetic relatedness, not aquatic habitat, strongly influences HTT rates.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

GenomeDelta identifies recent transposable element invasions and other novel sequences without a repeat library, validated with simulated and real data.

The paper shows that heat stress increases LTR retrotransposon transcription in Macrostomum lignano by hijacking the heat shock response pathway, a mechanism previously known in plants.

This paper presents the first chromosome-level genome assembly of Mastigoproctus giganteus, revealing evidence of an ancient whole genome duplication.

This study uses whole-genome sequencing to show that LINE-1 retrotransposition directly causes chromosomal rearrangements and instability in cancer genomes.

The paper uses immunolocalization of KNL1 to accurately determine the chromosome number of six Vellozia species, finding 2n = 18 and x = 9, correcting previous discrepancies.

The paper shows that giant transposons in fungi acquire beneficial genes through horizontal gene transfer, enabling rapid adaptation.

The paper shows that AFD neuron dysfunction in C. elegans alters transposable element (TE) expression, with Mirage transposase induction being a consistent phenotype, while Tc1 mutagenesis depends on background factors.

The paper analyzes sequence repeats and secondary structures in ITS1 and ITS2 of rDNA from catfish species to identify molecular signatures for species characterization.

This study estimates rates of chromosome number evolution in birds, finding higher fusion rates and a correlation between micro- and macrochromosome rearrangements, with population size and selection influencing these patterns.

CDR-Finder identifies hypomethylated regions in centromeres using long-read sequencing data and generates BED files and plots for analysis.

This study compares hybrid male sterility in two rodent crosses, finding stage-dependent misexpression and sex-chromosome overexpression, suggesting distinct mechanisms in dwarf hamsters and house mice.

This paper presents a high-quality genome assembly for the Chinese white truffle and analyzes TE dynamics and genome evolution in Tuberaceae.

The study investigates the role of the siRNA pathway in regulating transposable element expression in Aedes aegypti, finding limited impact in both somatic and gonadal tissues.

The paper develops a chromosome-scale reference genome and genetic map for yellow starthistle, identifies QTLs associated with invader traits, and finds structural variants and paleolog enrichment linked to invasion-related adaptations.

SatXplor is a pipeline for analyzing satellite DNA in complex genomes, offering tools for annotation, variation evaluation, and genomic context analysis.