genome assembly

Genome and methylome of the root crop table beet (Beta vulgaris)

The paper presents a chromosome-scale genome and methylome assembly for table beet, identifies candidate genes for geosmin production, and compares it with sugar beet.

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

This paper presents a chromosome-scale genome assembly for rubber dandelion, identifies key rubber pathway genes, and links chromosome reorganization to domestication traits.

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

This study uses PacBio HiFi sequencing to assemble complete Plasmodium falciparum genomes from natural infections, revealing full repertoires of immune-related genes.

Chromosome-level Atlantic switchgrass assemblies reveal a supernumerary B-Chromosome with transcriptional and evolutionary impacts

The paper identifies a supernumerary B-Chromosome in Atlantic switchgrass, showing its evolutionary origin and impact on gene expression and genomic diversity.

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

The paper presents a chromosome-level, haplotype-resolved genome assembly for the European moose, achieving high completeness and gene annotation.

Chromosome-scale nuclear and mitochondrial genome assemblies reveal extreme genome compartmentalization in the hazelnut pathogen Anisogramma anomala

The paper presents a chromosome-scale genome assembly of Anisogramma anomala, revealing extreme genome compartmentalization and unique mitochondrial features.

A finished, telomere-to-telomere assembly for Botrytis cinerea strain B05.10

The paper presents an improved genome assembly for Botrytis cinerea strain B05.10 with added telomeres and error corrections.

Haplotype-resolved genetic mapping using selfed progeny enables simultaneous genome assembly validation and trait dissection in a heterozygous plant

This paper introduces HRGM, a method that uses selfed progeny and haplotype-resolved assemblies to create genetic maps and validate genome assemblies in plants, identifying loci associated with root development.

Interactions between thermal and nutritional stress reveal cryptic adaptive potential

This study shows that adaptive potential in Drosophila depends on interactions between temperature and nutritional stress, revealing environment-dependent genetic variation.

Reversible fixation of microbial cells for targeted genomics

This paper introduces DSP as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction, improving targeted microbial genomics.

Genome-wide LD scores enable robust heritability and genetic correlation estimation from summary statistics across genetic ancestries

SUMMIT improves heritability and genetic correlation estimation across diverse ancestries using LD scores and GWAS summary statistics, showing better accuracy in non-European populations.

A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

Local population genetic structure of Andrena flavipes (Hymenoptera, Andrenidae), a nest-philopatric communal mining bee, reveals isolation-by-distance and high inbreeding

The paper assesses genetic structure and inbreeding in Andrena flavipes bees using SNPs, finding isolation-by-distance and high inbreeding despite high genetic variation.

An ONT sequencing framework for hantavirus genome assembly, variant analysis, and defective viral genome characterization from whole-segment amplicons

This paper introduces an Oxford Nanopore sequencing framework for hantavirus genome assembly and variant analysis, revealing defective viral genomes as a new feature of hantavirus populations.

Capturing Spatial Heterogeneity Using UAV-Derived Multispectral Phenotypes and Random Regression Models Improves Genetic Evaluation in Alfalfa Breeding Trials

Genomes of three Sympatric Species of an Adaptive Radiation: Cyprinodon variegatus, C. desquamator, and C. brontotheroides

The paper presents high-quality reference genomes for three sympatric Cyprinodon pupfish species to study speciation mechanisms and genomic architecture.

Chromosomal-Level Whole Genome Assemblies of Crassostrea Virginica

The paper generates a chromosome-level reference genome for Crassostrea virginica using PacBio HiFi, Illumina, and Hi-C data, achieving high completeness and reduced duplication.

Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci

The paper presents a chromosome-level genome of a type B avocado cultivar, identifies structural variations at flowering-type loci, and predicts the flowering type of a West Indian accession.

Decoding the naked mole-rat genome, telomere to telomere

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

Chromosome-level genome assembly of Falcataria falcata provides insights into ancient polyploidy and duplicate gene evolution in Fabaceae

This study presents a chromosome-level genome assembly of Falcataria falcata to investigate ancient polyploidy and duplicate gene evolution in Fabaceae, finding evidence for both ancestral and lineage-specific WGD events.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

Population structure of human-infecting and environmental isolates of Coccidioides immitis, the fungus causing Valley fever

The paper analyzes genetic structure and diversity of Coccidioides immitis in environmental and human isolates to understand disease transmission and environmental distribution.

Lateral flow devices can fast-track rabies virus genomic surveillance

This paper demonstrates that lateral flow devices can be used for rabies virus genomic surveillance, enabling rapid and decentralized genome collection without additional sample collection.

Genomic Insights into the Decline and Resilience of European Grayling in Switzerland

This study uses whole-genome resequencing to analyze genetic diversity and structure in Swiss grayling populations, revealing population declines, admixture, and limited genetic contribution from hatchery releases.

PoLoCo: A reproducible pooled low-coverage workflow for draft genome assembly and allele frequency analysis from ethanol-preserved small non-model invertebrates

A silent intergenic locus for efficient and versatile transgene expression in Plasmodium falciparum

The paper identifies a silent intergenic locus in Plasmodium falciparum that allows stable transgene expression without disrupting native genes, enabling versatile genetic engineering.

A versatile set of computational tools for inference of genetic ancestry from human molecular data

The paper introduces RAIDS, a toolset for inferring genetic ancestry from various sequence data, including cancer and low-coverage scenarios.

High temperature ligation enables in vitro assembly of eukaryotic genes

This paper introduces High Temperature (HighT) assembly, a DNA assembly method that improves accuracy and yield by ligating DNA at higher temperatures, and demonstrates its application in constructing synthetic genes and genomic regions.

Cromosomal genomes assemblies of twelve sheep breeds

The paper assembles high-quality genomes for twelve sheep breeds using long-read sequencing and phased haplotyping, enabling pangenome construction and structural variant analysis.