variant calling

Population Genomics of the Bovine Sialic Acid Network Reveals Functional and Evolutionary Diversity Across European and South African Cattle Breeds

The paper characterizes genetic variation in the bovine sialic acid network across European and South African cattle breeds, identifying 15 prioritized protein-altering variants and highlighting population differences.

WheatPanRef: a unified linear pan-reference genome for wheat genomics

WheatPanRef provides a unified linear pan-reference genome for wheat, improving read alignment and enabling integration of genomic resources across diverse accessions.

Genomic prediction of resistance to Phytophthora megakarya in cacao from a sparse host-pathogen screen

This study predicts cacao resistance to Phytophthora megakarya using genomic data, finding that host genomic relationships are more predictive than pathogen relatedness in a structured host-pathogen system.

Cell-in-drop genotyping detects megabase-scale loss of heterozygosity as a quantitative marker for CRISPR-Cas9 on-target toxicity

A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

Asymmetric migration shapes genetic structure of the invasive avian vampire fly (Philornis downsi) across the Galapagos Islands.

This study investigates the genetic structure and dispersal patterns of Philornis downsi across Galapagos Islands using whole genome sequencing, finding asymmetric gene flow and genetic divergence linked to trade winds and shipping routes.

Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii

This paper develops a CRISPR-Cas9 system for Anaerocellum bescii, enabling gene deletions and vector maintenance through thermostable Cas9.

Rescued from extinction in two buckets: genomic consequences of an extreme bottleneck in the endangered Owens pupfish

The paper analyzes the genomic consequences of a severe bottleneck in Owens pupfish, finding reduced genetic diversity and a 17-fold contraction in effective population size, but low recent inbreeding due to population expansion.

Reaction Norm Modeling of High-Dimensional Genomic and Environmental Data Improves Prediction Accuracy in Winter Wheat

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

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.

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.

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.

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.

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.

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.

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.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae)

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

RASTRO: Branching Point Decision-Making in Unitig Graphs

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus)

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

PfPHAST: Plasmodium falciparum Public Health Amplicon Sequencing Tool, a Streamlined Panel for Malaria Genomic Surveillance

PfPHAST is a streamlined amplicon sequencing panel for malaria genomic surveillance, offering better quality control and cost efficiency than MAD4HatTeR without sacrificing performance on shared targets.