Chromosomal and Genetic Variations

Transposable element activity and polymorphisms drive structural variability within and between individual in bivalves

This study identifies structural variants and transposable element insertions in oysters, showing their role in genomic diversity and adaptation to environmental conditions.

Regulatory Subfunctionalization drives OXPHOS evolution in teleosts

The paper investigates how regulatory subfunctionalization of OXPHOS paralogs contributes to ontogenetic plasticity in teleosts following whole genome duplication events.

A simple and accurate method for inferring missing ploidy information from sequence data

This paper introduces a machine learning method to infer ploidy from sequencing data, achieving high accuracy on simulated and empirical datasets.

The eumetazoan origin of PRDM9 function revealed by cnidarian genome analysis

The study identifies functional PRDM9 orthologs in cnidarians, revealing evolutionary dynamics and suggesting an ancient origin of PRDM9 function.

NLR DNA copy-number expansion outpaces accumulation of predicted coding-intact copies

The paper compares NLR DNA copy-number expansion with predicted coding-intact copies in Capsicum and Arabidopsis genomes, finding sublinear scaling and heterogeneous coding recovery.

PRDM9 Alleles Guide Distinct Patterns of Recombination Localization in Atlantic Salmon

The paper shows that different PRDM9 alleles in Atlantic salmon lead to distinct recombination patterns, similar to what is seen in mammals.

A developmental switch in the piRNA pathway ensures stage-specific transposon silencing

The paper shows the piRNA pathway in Drosophila undergoes a developmental switch to target different transposon families at distinct germline stages.

The maize recombination landscape evolved during domestication.

This study shows that maize evolved a higher recombination rate and re-patterning of crossover events during domestication, which enhanced genetic diversity and adaptation.

Tinkering loci: hubs of gene birth in an animal genome

The paper identifies 'tinkering loci' in Drosophila genomes that accelerate gene birth by concentrating duplicated gene fragments and facilitating composite gene creation.

A chromosome-scale genome assembly of the Swiss Lolium multiflorum ecotype Tremona reveals a scalable method to purge spurious duplications

The paper presents a chromosome-scale genome assembly of L. multiflorum and introduces ParaLies, a tool that reduces spurious duplications in highly heterozygous genomes.

Unmasking the large and highly repetitive genome of Phlox reveals a complex evolutionary history of speciation with gene flow

The paper presents chromosome-level genome assemblies and population genetic data for three Phlox species, revealing extensive genetic variation and widespread gene flow during speciation.

Reconstruction of the gastropod ancestral karyotype reveals lineage-specific chromosomal evolution and adaptations during habitat transitions

This paper reconstructs the ancestral gastropod karyotype and shows lineage-specific chromosomal strategies associated with habitat transitions.

Lens species genome assemblies reveal evolutionarily fragile chromosomes associated with pericentric inversions

The paper assembles genomes of seven Lens species and identifies fragile chromosomes linked to pericentric inversions and centromere diversity.

A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution

This study presents the first telomere-to-telomere genome of Manilkara zapota, revealing repeat-mediated genome evolution and epigenetic regulation of transposable elements.

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

The paper presents a high-quality genome assembly of the sea stickleback and reveals chromosomal fusions and fissions that reshape understanding of karyotype evolution in sticklebacks.

Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid

This study examines nonadditive gene expression and homoeolog expression bias in hexaploid wheat hybrids, finding widespread nonadditive expression and altered homoeolog balance linked to parental divergence and gene body methylation.

Direct cell-to-cell transmission of retrotransposons

The paper identifies a noncanonical retrotransposon transmission mechanism in Drosophila that bypasses the need for viral envelope proteins.

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution

The paper analyzes telomere-specialized transposons across Drosophila species, revealing rapid evolution, convergent loss, horizontal transfer, and gene capture mechanisms.

Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs

The paper identifies SNPC-1.2 as a female-specific piRNA transcription factor in C. elegans, revealing how gene duplication and functional specialization generate sex-specific piRNA expression.

Evolutionary persistence of a highly prevalent multicopy mitochondrial-derived nuclear insertion (Mega-NUMT) in Neotropical Drosophila flies

The paper identifies a high-prevalence Mega-NUMT in Drosophila paulistorum using long-read sequencing, suggesting its persistence due to balancing selection.

The evolutionarily conserved C-terminal domain of a domesticated transposase-derived protein regulates its DNA integration ability

This study investigates the evolutionary and functional role of the C-terminal domain in THAP9 and DmTNP, showing conserved structural elements and a non-essential role in DNA transposition.

Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm

This study investigates the genetic basis of heterosis in hybrid oil palm by analyzing haplotype-resolved genomes and transcriptomes, revealing complementary gene expression and regulatory mechanisms.

Adaptive deletion of functional duplicate genes in Drosophila

This study shows gene deletion in Drosophila preferentially removes functionally unique, younger duplicates rather than degenerate ones, suggesting an adaptive role in genome streamlining.

Utilising nuclear encoded plastid DNA to identify donors of grass-to-grass lateral gene transfer

This study identifies donor species of grass-to-grass lateral gene transfer using nuclear-encoded plastid DNA, finding two lateral acquisitions from specific lineages.

Massive programmed DNA elimination during embryogenesis in the trioecious nematode Auanema rhodense

The paper reports extreme programmed DNA elimination in Auanema rhodense during embryogenesis, revealing extensive loss of germline-specific DNA from somatic cells.

Selection shapes the evolution of genome size in a globally invasive plant

The paper examines genome size and transposable element abundance in invasive common ragweed across native and invasive ranges, finding range-specific selection and environmental correlations.

Scale dependence decouple life history traits from transposable element evolution in sauropsids

The paper tests proxies for effective population size in sauropsids and finds they poorly predict transposable element dynamics within clades.

Evolution of transposons as controlling elements

This study shows that transposases can act as transcriptional regulators and evolved into transcription factors through loss of catalytic activity.

The Little Transib That Could -- and Could Not: Contrasting Invasion Outcomes within a Novel DDE DNA Transposon Lineage

The paper identifies and characterizes two related Transib elements in Drosophila, showing contrasting invasion patterns and genomic impacts.

The genetic control of rapid genome content divergence in Arabidopsis thaliana

This study identifies genetic factors influencing repeat abundance variation in Arabidopsis thaliana genomes using resequencing and genome-wide association analyses.