genome assembly

Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms

This paper shows that incorporating prior knowledge of sequence context-driven DNA fragmentation probabilities improves de novo genome assembly, especially for ultrashort reads.

Population Genomics of P. miniata along the Pacific Coastline Reveal Subtly Diverging Genomics Along an Extensive Range Gap

This study uses whole-genome sequencing to show genetic disjunction and divergence in the bat star Patiria miniata despite its long-lived planktonic larvae, suggesting recent ecological or oceanographic barriers.

Chromosomal genome assemblies of Antarctic Notothenia coriiceps and temperate relative Paranotothenia angustata

The paper presents chromosome-scale genome assemblies for two notothenioid fish species, providing insights into their evolutionary history and adaptation to climate change.

A de novo reference genome of the golden jackal, Canis aureus

The paper presents the first chromosome-level genome assembly of the golden jackal using PacBio HiFi sequencing, providing a resource for studying its genetics and ecological impact.

The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology

The paper presents a high-quality genome assembly of Drosophila melanogaster ovarian somatic cells to study piRNA biology and transposon control.

GENOMIC ADAPTATION OF AN AUTOCHTHONOUS CIDER YEAST STRAIN TO BUCKWHEAT AND BARLEY WORT UNDER STRESSFUL BREWING CONDITIONS

This study uses adaptive laboratory evolution to domesticate cider yeast for efficient fermentation of buckwheat and barley worts under stressful brewing conditions, resulting in genomic and phenotypic changes similar to traditional beer yeasts.

Genome assemblies of Indian desi cattle reveals hotspots of rearrangements and immune-related genetic diversity

This study presents high-quality genome assemblies of five Indian desi cattle breeds, identifying immune-related genetic diversity and rearrangement hotspots.

Genome sequence assembly and annotation of MATA and MATB strains of Yarrowia lipolytica

The paper presents high-quality genome assemblies and annotations for two Yarrowia lipolytica strains, using a combination of short-read and long-read sequencing technologies.

Comparing the genetic diversity of two threatened Rhyticeros hornbill species with contrasting geographic range sizes

The paper compares genetic diversity between two hornbill species, finding the island-endemic Narcondam Hornbill has significantly lower genetic diversity than the Wreathed Hornbill.

LOBSTERS: a modular vector series with a diverse set of Cas nucleases and plasmid selection markers for multiplex genome editing in Saccharomyces cerevisiae

LOBSTERS provides a modular CRISPR system with diverse Cas nucleases and plasmid markers for efficient multiplex genome editing in yeast.

A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

The paper assembles a gap-free telomere-to-telomere pig genome, revealing new genes, structural variations, and insights into centromere evolution and breed-specific selection.

Characterising Staphylococcus aureus genomic epidemiology with Multilevel Genome Typing.

This study develops a multilevel genome typing (MGT) scheme for Staphylococcus aureus to characterize genomic epidemiology at various scales using 50,481 genomes.

A pan-generic marker panel for apples to enable genetic research and breeding across Malus species

The paper develops a pan-generic 3K DArTag marker panel for Malus species to enable genetic research and breeding, showing strong cross-species transferability and utility for QTL mapping and marker-assisted selection.

Comparison of genomic assembly and annotation based on two clones of avian pathogenic Escherichia coli

The paper compares genomic assembly and annotation methods for two clones of avian pathogenic Escherichia coli using short and long-read sequencing.

Histo-LCM-Hi-C reveals the 3D chromatin conformation of spatially localized rare cells in tissues at high resolution

The paper introduces Histo-LCM-Hi-C to study 3D chromatin structure of rare tissue cells, showing distinct chromatin organization in liver Kupffer cells compared to whole liver and in vitro macrophages.

Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha.

This paper introduces a tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha, improving efficiency and scalability of genome modifications.

Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler

Alice is a fast, memory-efficient long-read assembler that enables strain-resolved metagenomic analysis of large datasets with significant speed and resource improvements over existing methods.

Harnessing genome prediction in Brassica napus through a nested association mapping population

This study evaluates genome prediction accuracy in Brassica napus using nested association mapping, finding that rrBLUP and RKHS models and SNaP markers improve prediction accuracy for agronomic traits.

First Genome-Wide Centromere Map of Trypanosoma cruzi Reveals Linear and 3D Compartment Boundaries and Spatial Clustering

The paper generates a high-quality genome assembly and centromere map for T. cruzi using Hi-C and ChIP-seq, revealing structural boundaries and 3D clustering of centromeres.

Enhancing genome recovery across metagenomic samples using MAGmax

MAGmax improves genome recovery in metagenomic samples by merging and reassembling bins, producing higher-quality MAGs faster and with less memory than dRep.

Chromosome-level genome assembly for Sichuan taimen (hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage

The paper presents the first chromosome-level genome assembly for Sichuan taimen, revealing high tandem repeat proportions and population shrinkage.

Dual transposon sequencing (Dual Tn-seq) to probe genome-wide genetic interactions

The paper introduces Dual Tn-seq to assess genome-wide genetic interactions in Streptococcus pneumoniae by analyzing double mutants, revealing new biochemical pathway components.

HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids

HaploCharmer is a Snakemake workflow for read-scale haplotype calling in polyploids, validated on sugarcane and Saccharum data, identifying high-quality haplotypes with low false positives.

The formation and propagation of human Robertsonian chromosomes

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

Genetic diversity and variation in heterozygosity in Macadamia

This study analyzes genetic diversity and heterozygosity in Macadamia species using whole-genome sequencing, finding reduced diversity in domesticated varieties and a correlation between heterozygosity and yield efficiency.

Reference genome choice compromises population genetic analyses

This study shows that using a conspecific reference genome improves variant detection and genetic diversity estimates compared to heterospecific references in gray foxes.

Diploid assembly of the Mexican lime genome reveals extensive heterozygosity

The paper assembles the diploid genome of Mexican lime, revealing high heterozygosity and structural variants between thorned and thornless lineages.

REWRITE Enables Locus-Scale Engineering of Synthetic HLA Haplotypes in Human Pluripotent Stem Cells

REWRITE enables scar-minimized rewriting of native human loci exceeding 100 kb in hPSCs, demonstrated through synthetic refactoring of the class-I HLA region.