genome assembly

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

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.

Evaluation of a multiplexed tiling PCR scheme for whole-genome amplification of hepatitis B virus using Oxford Nanopore sequencing

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.

A haplotype-resolved bluethroat (Luscinia s. svecica) genome assembly uncovers the complex MHC region

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

Rapid CRISPR-Cas9 Genome Editing in S. cerevisiae

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

The diploid reference genome of a human embryonic stem cell line

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 relationship between genomic variation and genetic load: insights from small island populations

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.

Unlocking the potential of Capsicum Germplasm Collections for Climate Resilience and Fruit Quality

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

Nuclear genome profiling of two species of Epidendrum (Orchidaceae): genome size, repeatome and ploidy

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.

Soil composition structures genetic variation across small spatial scales in a rare serpentine endemic plant

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

Whole genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases

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.

Adaptive sampling-based enrichment enables genome reconstruction of intracellular symbionts despite host background and reference divergence

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.

High-resolution metagenome assembly for modern long reads with myloasm

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

A Trypanosome Trifecta: an independently tunable triple inducer system for genetic studies in Trypanosoma brucei.

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

Replicated hybrid zones reveal genomic patterns of local adaptation and introgression in spruce

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.

Ancient human genomes from the Altai region reveal population continuity and shifts in the 4th-12th centuries

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.

A chromosome-level assembly of the Fusarium oxysporum biocontrol strain FO12

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.

The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events

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

A near chromosome-scale genome assembly of the Common pine sawfly (Diprion pini, Linnaeus, 1758)

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 population structure and genetic health of European wolves

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.

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

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

The 3D Genome of Gigaspora margarita Unveils Stable Chromatin and Nucleolar Organization and Symbiont-Dependent Genome Dynamics

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

The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates

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

NOHIC: A PIPELINE FOR PLANT CONTIG SCAFFOLDING USING PERSONALIZED REFERENCES FROM PANGENOME GRAPHS

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

Chromosome-level Genome Assembly of the South African Lion (Panthera leo melanochaita)

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

Characterizing Co-Circulating Respiratory Virus Genomic Diversity in Switzerland with Hybrid-Capture Sequencing and Phylogenetic Reconstructions: Insights into the 2023/24 Season

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

The genome of the reef-building coral Porites harrisoni from the southern Persian/Arabian Gulf

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: A Multi-Kingdom Trajectory Architecture for Genomic Prediction with Evolutionary Curriculum Learning

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

Genome assembly and annotation of the naked mole rat Heterocephalus glaber reared in Japan

This study generates a new genome assembly for Japanese-reared naked mole rats, identifies novel gene models and genomic variations, and provides functional annotations.

First draft genome of the decaploid species, Ludwigiagrandiflora subsp. hexapetala, validated through geneexpression

The paper presents the first draft genome of the invasive Ludwigia grandiflora subsp. hexapetala, validated through gene expression analysis, and identifies a large number of protein-coding genes.

Enabling Plasmid-based Expression in Clostridium kluyveri using a Biparental Methylation-Conjugation System

This paper develops a methylation-conjugation system for Clostridium kluyveri to enable plasmid-based genetic modification and demonstrates its use for expressing a fluorescent reporter.