genome assembly

The paper analyzes genome data from spittlebugs in vineyards and quasi-natural populations, revealing cryptic population structure, life-history divergence, and insecticide resistance.

The paper uses ddRADSeq to analyze genetic structure in southern flounder over multiple years, finding significant differentiation between regions and temporal variability within estuaries.

This paper introduces Mikado, a method using sparse linear algebra to accelerate genotype representation graph computations, significantly improving speed over existing tools on large biobank datasets.

The paper presents the first chromosome-level nuclear genome of Simulium vittatum, linking cytogenetic features to genome organization and evolution.

LongPhase-TO reconstructs somatic haplotypes from tumor-only long-read sequencing, improving variant calling accuracy and haplotype block size.

This study uses whole-genome sequencing to analyze genetic connectivity among queen conch populations in US Caribbean waters, finding a connected system with substantial gene flow and geographic differentiation.

This study examines genetic diversity and population structure in small island populations of the Turks and Caicos rock iguana, finding low genetic diversity but limited inbreeding and suggesting a low threshold for population persistence.

The paper uses whole genome sequencing to analyze the genetic structure of a Greek-speaking community in Southern Italy, finding no strong evidence for external origins and supporting a model of continuous gene flow.

The paper generates chromosome-level assemblies of the mountain pine beetle to study neo-sex chromosome evolution, revealing rapid degeneration and structural divergence in neo-Y chromosomes.

The paper presents a high-quality chromosome-level genome assembly of the Arabian killifish, providing a genomic resource for comparative genomics studies.

The paper presents a high-quality genome assembly for the green-bronze dung beetle, Onthophagus orpheus, and annotates its genes for future ecological and genetic studies.

The paper introduces pTRIP, a new integrative plasmid for Listeria monocytogenes that allows stable gene integration without antibiotic selection.

This paper presents a chromosome-level, haplotype-resolved genome assembly of big trefoil using CiFi, revealing two phased haplotypes and supporting gene annotation.

The paper discovers and engineers an orthogonal translation system using metagenomic data to expand the genetic code with non-canonical amino acids.

The paper compares damage correction methods for ancient DNA libraries to assess their impact on imputation and kinship inference.

This paper develops a modular click-chemistry strategy to modify CRISPR RNPs without disrupting their formation, enhancing DNA accessibility and enabling genome imaging.

This paper presents a chromosome-level genome assembly for Helichrysum odoratissimum to support genetic and functional studies.

PePApipe is a bioinformatics pipeline for ASFV genome analysis that integrates multiple tools into an automated workflow, enabling rapid and reproducible genomic analysis with minimal bioinformatics expertise.

This paper uses quantum computing to assemble a large genome on current hardware, achieving high accuracy despite technical limitations.

This study examines genetic correlations between reproduction and longevity in historical Dutch cohorts, finding weak or mixed evidence for a fertility-longevity trade-off.

The paper uses whole-genome sequencing to identify neutral and adaptive variation in two albatross species, revealing genetic differentiation and local adaptation.

This paper presents a high-quality chromosome-level genome assembly of Daphnia magna using PacBio HiFi sequencing, resolving scaffolding issues and providing gene expression profiles for comparative genomic studies.

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

The paper introduces PAT, an AI tool for automated pollen viability analysis, and uses it to identify a genetic suppressor of meiotic defects in Arabidopsis.

This study identifies a QTL on chromosome 4 associated with circadian feeding rhythmicity in pigs, linking it to genes involved in feeding behavior and energy homeostasis.

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

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

The paper develops a low-cost genotyping panel for Yesso scallops to support breeding and disease resistance studies.

The paper evaluates genetic diversity within and between sugarcane families using microsatellite markers and distances to account for polyploidy, finding most variation is within families.