genome assembly

A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

The paper presents a haplotype-resolved genome of Quercus alba and analyzes its genetic diversity and phylogenetic relationships within oaks.

ERGA-BGE genome of Coenonympha oedippus: an IUCN endangered European butterfly species occurring in two ecotypes

The paper presents the reference genome of Coenonympha oedippus, an endangered butterfly, to study genetic mechanisms of adaptation to two ecotypes and support conservation efforts.

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

The paper demonstrates long-read sequencing and genome assembly of ethanol-preserved samples, including challenging organisms like the maned sloth, achieving a 3.1 Gb assembly.

WISER: an innovative and efficient method for correcting population structure in omics-based selection and association studies

WISER improves phenotype estimation in omics studies by correcting population structure, outperforming LS and BLUP across multiple species and datasets.

Genomic Characterization of Novel Endophyte Strains from Tall Fescue Shows Genome Fragmentation Post-Hybridization

This study characterizes the genomes of two novel Epichloe hybrid strains, showing fragmentation and rearrangement post-hybridization but retention of most gene homologs.

The Silene latifolia genome and its giant Y chromosome

This study sequences the giant Y chromosome of Silene latifolia and reveals its structure, function, and evolutionary history.

Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani

The paper analyzes the genome of Fusarium solani strain SB1, revealing that dispensable genome regions and segmental duplications contribute to its genome plasticity and adaptive traits.

A genomic history of the North Pontic Region from the Neolithic to the Bronze Age

This study analyzes genomic data from 78 prehistoric North Pontic individuals to trace genetic ancestry and migration patterns from the Neolithic to the Bronze Age.

VRPG: an interactive visualization framework for reference-projected pangenome graph

VRPG provides an interactive visualization framework for pangenome graphs, enabling exploration, annotation, and comparison of genomic variation across species.

Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region

The paper presents chromosome-level genomes of three Amaranthus species, identifies a male-specific region, and characterizes genes and eccDNA related to sex determination and herbicide resistance.

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

This paper presents the first chromosome-level genome assembly and annotation for the red coral Corallium rubrum, providing genomic resources for conservation and population genomics studies.

An initial genome editing toolset for Caldimonas thermodepolymerans, the first model of thermophilic polyhydroxyalkanoates producer

This paper develops genome editing tools for Caldimonas thermodepolymerans, a thermophilic PHA producer, to enhance its biotechnological potential through genetic manipulation.

Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea

The paper presents the first genome assemblies for three Caribbean reef-building corals and explores genomic novelties, finding abundant gene duplications and a large genome size in Siderastrea siderea.

High-fidelity annotated genome of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii

The paper presents a high-quality genome assembly of Meloidogyne enterolobii using long-read sequencing and a gap-aware transformer model.

Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status

The paper surveys Ruminococcus gnavus distribution across host lifestyles and health, revealing higher prevalence in Westernized populations and genomic differences between healthy and Crohn's disease isolates.

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

Towards a universal foundation model for biobank-scale human genome variation

This paper introduces SNPBag, a foundation model for analyzing human genome variation, achieving state-of-the-art accuracy in genotype imputation and efficient ancestry inference.

Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome

The paper presents the chromosome-scale assembly of the giant Pleurodeles waltl genome, revealing insights into its expansion and regeneration-related genes.

Draft genome sequence of the glasshouse-potato aphid Aulacorthum solani

The paper presents a new draft genome of Aulacorthum solani, correcting contamination in the existing genome and providing functional annotations for most predicted genes.

Chromosome-level reference genome assembly for the mountain hare (Lepus timidus)

This paper presents a high-quality chromosome-level genome assembly for the mountain hare, contributing to the European Reference Genome Atlas initiative.

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues

This paper evaluates long-read sequencing for characterizing the OsHV-1 genome from infected M. gigas tissues, showing improved accuracy compared to short-read methods.

Genomic connectivity and adaptation signals of the freshwater sponge Ephydatia muelleri across its distribution

This study examines genetic connectivity and adaptation in Ephydatia muelleri across its range using ddRADseq data, finding low connectivity and polygenic adaptation to environmental factors.

Distinct Genetic Populations and Resistance Backgrounds of the Malaria Vector Anopheles funestus in Tanzania

The paper analyzes the population genetics of Anopheles funestus in Tanzania, identifying two distinct genetic populations with different resistance backgrounds and suggesting geographic barriers to gene flow.

Exploiting Endogenous CRISPR-Cas9 System for Functional Engineering of Probiotic Lacticaseibacillus rhamnosus GG (LGG)

This paper develops an endogenous CRISPR-Cas9 system for precise genome editing of LGG, enabling functional strain engineering for probiotic applications.

Unravelling termite evolution with 47 high-resolution genome assemblies

This study sequenced 47 termite genomes, revealing genomic expansions linked to dietary evolution and ecological success in Termitidae.

Limited genetic diversity among Malassezia furfur isolates during two one-year neonatal and pediatric bloodstream infection surveys confirms preference for one specific IGS1 genotype in deep-seated infections

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

The paper presents the genome of Pinctada radiata, a Lessepsian migrant, providing insights into its genetic adaptations to environmental changes and supporting conservation efforts.

Genome Sequencing, Molecular Marker Development and Genetic Diversity Assessment of Economically Important Vulnerable Tree Species Saraca asoca (Roxb.) W.J de Wilde

This study sequences the genome of Saraca asoca and assesses genetic diversity using GBS, identifying SSRs and biosynthesis pathways for flavonoids.

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

The paper uses genome sequencing to show genetic drift impacts bull and giant kelp populations, with no purging of harmful alleles, and suggests conservation strategies.