genome assembly

This paper improves genomic prediction accuracy in winter wheat by integrating genotype-by-environment interactions and environmental covariates across multiple environments.

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.

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

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

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

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

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

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

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

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.

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

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

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

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

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

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.

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

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.

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.

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.

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

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

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.

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.

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

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

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.