genome assembly

Chromosome-level genome assembly of the Brazilian merganser (Mergus octosetaceus), a rare and elusive waterfowl species

The paper presents the first chromosome-level genome assembly of the Brazilian merganser, revealing genomic features and population history insights.

Chromosome-level assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome

The paper assembles and annotates the first chromosome-level nuclear reference genome of the grey reef shark using long-read sequencing, providing a resource for evolutionary and conservation studies.

Genome assembly of five Tephritid species for the enhancement of the Sterile Insect Technique

The paper presents chromosome-level genome assemblies for five Tephritid species using long-read sequencing, short-read polishing, and Hi-C scaffolding.

The complementary roles of rare variant burden scores and common variant polygenic risk scores in genetic risk prediction of complex disorders

This study combines rare variant burden scores and common variant polygenic risk scores to improve genetic risk prediction for schizophrenia, hypertrophic cardiomyopathy, and major depressive disorder.

A Cas12a Toolbox for Rapid and Flexible Group B Streptococcus Genomic Editing and CRISPRi

This paper develops a Cas12a-based toolkit for efficient genomic editing and CRISPRi in Group B Streptococcus, enabling targeted gene modifications and inducible gene silencing with minimal off-target effects.

Checkpoint-dependent sensitivities to nucleoside analogues uncover specific patterns of genomic instability

This study tests the effects of nucleoside analogues on fission yeast with DNA replication checkpoint mutations, revealing sensitivity patterns and potential clinical implications.

Telomere-to-telomere gap-free genome assembly of a male donkey and the identification of novel SVs associated with functional genes

The paper presents a gap-free donkey genome assembly and identifies novel structural variants in functional genes.

Integrating three genetic dimensions relating to piglet birth weight: direct and maternal effects on the mean and genetic control of residual variance

This paper estimates direct and maternal genetic effects on piglet birth weight and its variability, finding maternal effects are crucial while direct effects are negligible.

Learning genetic values of individuals with incomplete pedigree, genomic and phenotypic data

The paper introduces Hy-BLUP, a Bayesian prediction method for handling incomplete pedigree, genomic, and phenotypic data in genome-enabled prediction.

Genome assembly and annotations of a Cyprinidae fish, Sinibrama wui

This study presents a high-quality chromosome-level genome assembly of Sinibrama wui and identifies expanded gene families related to lipid metabolism and nervous system.

Ultra-high field strength electroporation enables efficient DNA transformation and genome editing in nontuberculous mycobacteria

This paper introduces ultra-high field electroporation to improve DNA transformation and genome editing in non-tuberculous mycobacteria, achieving significant efficiency gains in multiple species.

Unmasking Vibrio paracholerae: Genomic Reclassification and Epidemiology

This study reclassifies 193 genomes as Vibrio paracholerae using genomic analysis and identifies its virulence factors and antibiotic resistance genes.

Drift and isolation drive genomic erosion and island speciation in a lineage of macaques

The paper shows that island isolation and genetic drift rapidly drive speciation in macaques, leading to genomic divergence, loss of diversity, and adaptive mutations.

Improved genome assembly of whale shark, the world's biggest fish: revealing "chromocline" in intragenomic heterogeneity

The paper presents an improved chromosome-level genome assembly of the whale shark, revealing a chromocline effect in substitution rates across chromosomes.

Establishment of an antimetabolite-based transformation system for the wood-decaying basidiomycete Phanerochaete chrysosporium

This paper establishes an antimetabolite-based transformation system for Phanerochaete chrysosporium, enabling efficient genetic manipulation and heterologous gene expression.

First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity

The paper assembles and annotates the first whole genome of the ball python (Python regius), providing a high-quality resource for studying snake-specific traits and physiological adaptations.

Just add water: A simple floral bud injection method for stable Agrobacterium-mediated transformation in two ecotypes of Mimulus guttatus

The paper introduces a floral injection method to improve Agrobacterium-mediated transformation in Mimulus guttatus, enabling transformation of both coastal perennial and inland annual ecotypes.

Multi-millennial genetic resilience of Baltic diatom populations disturbed in the past centuries

This study analyzes the genetic stability and resilience of Baltic diatom populations over 8000 years, showing accelerated genetic change linked to historical human activity.

From Fragmentation to Resolution: High-Fidelity Genome Assembly of Zancudomyces culisetae through Comparative Insights from PacBio, Nanopore, and Illumina Sequencing

This paper generates a high-quality genome assembly for Zancudomyces culisetae using PacBio-HiFi sequencing and evaluates sequencing technologies for fungal genome assembly.

Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data

This study improves genomic prediction of stalk lodging resistance in maize by integrating multi-environment data, showing that multi-environment models significantly enhance prediction accuracy for most traits.

Genome structural plasticity and copy number dynamics shape adaptive evolution in a barley fungal pathogen

The paper presents a haplotype-resolved genome assembly of Puccinia hordei, revealing structural plasticity, copy number variation, and evolutionary dynamics in a barley fungal pathogen.

A Prelude to Conservation Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel (Pteromyini: Pteromys volans)

The paper presents the first chromosome-level genome assembly of the Siberian flying squirrel, providing insights into its evolutionary relationships and conservation genetics.

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

The paper presents chromosome-level genome assemblies for two wild cherry species, revealing structural variations and insights into their evolutionary relationships.

CRISPR/Cas9-mediated mutagenesis of the white-eye gene in the tephritid pest Bactrocera zonata

The paper develops a genetic tool for Bactrocera zonata by creating a chromosome-level genome and CRISPR/Cas9-induced white-eye mutants to aid in Genetic Sexing Strain development.

The genome of the Glacier lanternfish shows loss of MHC I and II function and provides insight into evolution of lanternfish immune systems

The paper presents the genome of the Glacier lanternfish, revealing loss of adaptive immune system genes and providing insights into immune system evolution in lanternfishes.

Optimizing storage, high-molecular weight DNA extraction and genome reconstructions from human faecal samples.

The paper evaluates DNA extraction and storage protocols for human faecal samples to optimize high-molecular weight DNA recovery for long-read metagenomics.

Variation in genome architecture and epigenetic modification across the microsporidia phylogeny

This study compares genome and epigenetic architecture across multiple microsporidia clades, finding limited conservation and significant variation in genetic features and epigenetic modifications.

Autocycler: long-read consensus assembly for bacterial genomes

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

Genomic insights into population stratification, biological adaptation, and archaic introgression at the crossroads of the Himalayas and lowland East Asia

The paper presents genomic data from 1,031 individuals in the Tibetan-Yi Corridor, identifying genetic variants, adaptation signatures, and archaic introgression patterns.

Equine herpesvirus myeloencephalopathy-related mutations in EHV-1 DNA polymerase allow EHV-1 to grow at elevated temperatures

The paper shows that EHV-1 strains with specific mutations in the DNA polymerase gene can replicate at elevated temperatures, linking these mutations to EHM.