genome assembly

Genetic manipulation of Bacteriophage T4 utilizing the CRISPR-Cas13b system

This paper describes a CRISPR-Cas13b-based method to edit the T4 bacteriophage genome, enabling gene deletions, mutations, and fluorescent protein insertion for studying phage biology.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

The paper presents a chromosome-level genome assembly and annotation of Cryptosporidium meleagridis, revealing 3,923 protein-coding genes and high completeness.

The Hitchhiker's Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction

This study evaluates optimal long-read data types and volumes for chromosome-level haplotype-resolved pangenome assembly, providing guidelines for sequencing platform selection and coverage.

A chromosome-level genome of the giant vinegaroon Mastigoproctus giganteus exhibits the signature of pre-Silurian whole genome duplication

This paper presents the first chromosome-level genome assembly of Mastigoproctus giganteus, revealing evidence of an ancient whole genome duplication.

The Emirati T2T-Level Pangenome: A Graph of 58 Complete Genomes

The paper presents a T2T-level pangenome of 58 Emirati genomes, revealing genomic diversity comparable to the Human Pangenome Reference Consortium.

Genomic prediction of metabolic content in rice grain in response to warmer night conditions

This study evaluates genomic prediction of metabolic content in rice grains under control and high night temperature conditions, finding moderate heritability and improved accuracy with non-additive models.

Closing the genome of Teredinibacter turnerae T7902 by long-read nanopore sequencing

The paper closes the genome of Teredinibacter turnerae T7902 using long-read nanopore sequencing, providing a complete circular genome sequence for comparative genomics and host-symbiont evolution studies.

Multi-omics analysis and genome-scale metabolic reconstruction of cattle Bos taurus for optimal production of cultured meat

This study performs multi-omics analysis and builds a genome-scale metabolic model for Bos taurus muscle cells to improve cultured meat production.

H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability

This study shows that H3.1K27M disrupts chromatin maturation, leading to TSK/TONSL activation and genomic instability in Arabidopsis.

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

This paper presents a chromosome-level, haplotype-resolved genome assembly for the Eurasian minnow, revealing haplotype diversity and structural variations.

Genomic-guided conservation actions to restore the most endangered conifer in the Mediterranean Basin

The paper uses genomic data to assess genetic diversity and mating patterns in Sicilian fir, identifying inbreeding and introgression risks and proposing conservation strategies.

Complete genomes of DNA viruses in faecal samples from small terrestrial mammals in Spain

The paper identifies 25 complete or near-complete DNA virus genomes from small terrestrial mammals in Spain, including 18 potential new species or types.

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study.

This study develops and applies SNP genotyping methods for the endangered southern damselfly, identifying challenges and demonstrating improved resolution for genetic structure and conservation analysis.

ERGA-BGE Reference Genome of the Striped Field Mouse (Apodemus agrarius), a Widespread and Abundant Species in Central and Eastern Europe

The paper presents a chromosome-level reference genome for the striped field mouse, providing resources for phylogenetic studies and understanding its geographical distribution.

From Pigments to Precision: Exploring Genetic Transformation and Genome Editing in Wheat and Barley

This study uses genetic tools to improve wheat and barley transformation and gene editing, showing both benefits and limitations of different approaches.

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The paper presents the first reference genome of Gluvia dorsalis, a sun spider, providing insights into its adaptation to arid environments and arachnid evolution.

Characterization of radiations-inducedgenomic structural variations in Arabidopsis thaliana

The paper characterizes radiation-induced genomic structural variations in Arabidopsis thaliana using long-read sequencing and identifies MMEJ as a repair mechanism induced by UV-B, UV-C, and protons.

Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveal the origins of gene content reduction in Dendroctonus

The paper presents a chromosome-level genome assembly of the southern pine beetle and identifies gene content reduction and annotation biases in the Dendroctonus clade.

Local Haplotype Classifiers enable Efficient, Flexible, and Secure Genotype Imputation and Downstream Analyses

The paper introduces a privacy-preserving genotype imputation method using haplotype classifiers, improving accuracy and throughput compared to linear models.

Fluorescence-based CRISPR interference system for controlled genetic repression and live single-cell imaging in mycobacteria

The paper develops and validates fluorescence-based CRISPRi tools for gene repression and live single-cell imaging in mycobacteria.

Towards AI-designed genomes using a variational autoencoder

This paper introduces a variational autoencoder to model bacterial genomes, demonstrating its ability to reconstruct and generate functional genome vectors with high accuracy.

Genome-wide diversity in lowland and highland maize landraces from southern South America: population genetics insights to assist conservation

This study analyzes genetic diversity in maize landraces from Northern Argentina using genome-wide SNPs, identifying two gene pools at risk of genetic erosion due to climate change.

De Novo Genome Assembly and Annotation for the Webbing Clothes Moth (Tineola bisselliella): A Globally Distributed, Economically Important Pest

This paper presents the first reference-quality genome assembly and annotation for the webbing clothes moth, Tineola bisselliella, providing a resource for studying keratin digestion and lepidopteran chromosome evolution.

Inferring long-term and short-term determinants of genetic diversity in honey bees: Beekeeping impact and conservation strategies

This study uses whole-genome sequences from four honey bee species to assess genetic diversity impacts of beekeeping and conservation strategies, revealing historical bottlenecks and genomic conservation.

Telomere-to-telomere, gap-free genome of mung beans (Vigna radiata) provides insights into domestication under structural variation

The paper presents a gap-free genome assembly of mung beans and identifies structural variations and selection pressures during domestication.

Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin, 1841)

The paper uses MDA to generate high-quality genomes for small organisms, achieving contiguous assemblies for C. elegans and L. squamata.

Himalayan whole-genome sequences provide insight into population formation and adaptation

The paper presents whole-genome sequences from 16 Himalayan populations to study population structure, adaptation, and genetic history, revealing early population divergence, shared adaptive haplotypes, and recent gene flow.

Chromosome level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invadingthe River Rhine

The paper presents a high-quality chromosome-level genome assembly for the invasive Caucasian dwarf goby, providing a foundation for studying its adaptive traits.

ZW sex chromosome structure in Amborella trichopoda

The paper presents a haplotype-resolved genome assembly of Amborella trichopoda, identifying a young ZW sex chromosome system with a 3-Megabase sex-determination region that shows limited degeneration.