genome assembly

The paper develops haplotype-resolved genome assemblies for Norwegian Red cattle to improve variant detection and genomic predictions.

The paper presents the first high-quality genome assembly of Firmina major, an endangered tree species, providing insights for conservation efforts.

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

The paper evaluates a tiling PCR primer scheme for HBV whole-genome amplification using Oxford Nanopore sequencing, finding uneven amplicon performance limits full-genome recovery.

The paper presents a haplotype-resolved genome assembly of a bluethroat, revealing structural complexity in the MHC region.

This paper describes a rapid CRISPR-Cas9 genome editing protocol for S. cerevisiae using PCR-based guide installation and seamless plasmid recircularization.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

The paper examines the relationship between genomic variation and genetic load in small island populations, finding that low genetic diversity does not always correlate with high genetic load.

This paper develops a framework combining genomic prediction and a large language model to select climate-resilient pepper cultivars from germplasm collections.

This study profiles the nuclear genomes of two Epidendrum species using flow cytometry and k-mer analysis, finding a 2.3-fold genome size difference and high retrotransposon content.

The paper investigates how fine-scale soil composition influences genetic variation in a rare plant species with limited distribution.

The paper compares variant calling performance between Illumina NovaSeq X Plus and Element AVITI sequencing platforms using whole genome sequencing of human tumor cell lines, finding comparable results with minor differences in specific genomic contexts.

This paper demonstrates that adaptive sampling-based sequencing enables efficient genome reconstruction of intracellular symbionts from host-dominated samples, achieving high completeness and revealing structural divergence from reference genomes.

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

This paper develops a triple inducer system in Trypanosoma brucei for independently regulating three genetic elements, demonstrating independent control and tunability.

The paper compares genomic patterns of adaptation and introgression in two replicated hybrid zones of spruce, finding similar differentiation and directional introgression despite different environmental gradients.

This study analyzes ancient genomes from the Altai region to show genetic continuity and shifts between the 4th and 12th centuries, including the spread of East Asian ancestry and a unique lineage with Ancient North Eurasian ancestry.

The paper presents a chromosome-level genome assembly of the biocontrol strain Fusarium oxysporum FO12 using Nanopore and Hi-C data, providing a high-quality reference for agricultural research.

This paper presents a chromosome-level genome assembly of cloudberry, revealing its octoploid origin through multiple polyploidization events involving four subgenomes.

This paper presents a near chromosome-scale genome assembly for the common pine sawfly using long-read sequencing technologies, highlighting its utility for pest management and evolutionary studies.

The paper analyzes 1,001 wolf genomes to reveal distinct evolutionary lineages and genetic health issues across Europe, highlighting the need for region-specific conservation strategies.

This paper presents a Nanopore-only workflow for diploid T2T genome assembly and haplotype-resolved 3D chromatin maps, achieving high accuracy without hybrid polishing.

This study presents a 3D genome assembly of Gigaspora margarita and its endobacterium, revealing stable chromatin compartments and symbiont-dependent genome dynamics.

This study presents a chromosome-anchored genome assembly of Asymmetron lucayanum, revealing genome architecture and gene evolution in cephalochordates.

noHiC is a reference-guided scaffolding pipeline that uses personalized references from pangenome graphs to improve plant contig assembly.

This paper presents a high-quality chromosome-level genome assembly of the South African lion using PacBio HiFi and Omni-C sequencing technologies.

The paper characterizes respiratory virus genomic diversity in Switzerland using hybrid-capture sequencing and phylogenetic analysis, identifying prevalent strains and evolutionary insights.

This paper presents the genome assembly of the coral Porites harrisoni from the southern Persian/Arabian Gulf, providing insights into its genomic architecture and thermal resilience.

BioWorldModel predicts multi-trait phenotypic distributions across fungi, plants, and animals using a unified architecture, outperforming species-specific baselines.