genome assembly

EASY-CRISPR: a toolbox for high-throughput single-step custom genetic editing in bacteria

EASY-CRISPR enables high-throughput, single-step genetic editing in E. coli using optimized guide RNAs and repair templates to construct genetic tools and mutant libraries.

Genome sequencing and physiological characterization of three Neoarthrinium moseri strains

This study sequenced the genomes of three Neoarthrinium moseri strains and characterized their metabolic potential, revealing high biosynthetic gene clusters and ecological versatility.

Accurate hybrid plasmids assembly with HyPlAs

HyPlAs improves plasmid assembly from hybrid sequencing data by classifying short-read contigs as chromosomal or plasmidic, outperforming Plassembler on bacterial samples.

G-quadruplex stabilization induces DNA breaks in pericentromericrepetitive DNA sequences in B lymphocytes

This study shows that G4-stabilizing drugs like pyridostatin cause DNA breaks and chromosomal rearrangements in B cells, with differential effects between primary and malignant cells.

Abundant genetic variation is retained in many laboratory schistosome populations

This study finds that laboratory Schistosoma mansoni populations retain abundant genetic variation, with implications for drug resistance studies and GWAS.

The PERPETUAL FLOWERING Locus: Necessary But Insufficient for Genomic Prediction of Runnerless and Other Asexual Reproduction Phenotypes in Strawberry

This paper shows that the PF gene explains only 22% of runnering variation in strawberries and demonstrates that genomic prediction for runnering is feasible.

Host replacement dynamics shape virulence and genome evolution in a plant RNA virus

This study examines how host replacement dynamics influence virulence and genome evolution in a plant RNA virus, showing that sudden transitions lead to faster virulence changes and more severe symptoms.

Genome Report: Genome of the Amazon Guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation

The paper reports the genome of the Amazon guppy, revealing conserved sex chromosomes and complete X chromosome dosage compensation despite Y chromosome degeneration.

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity

The paper reports new genome assemblies of Camelina species, revealing subgenome dominance patterns linked to chromosomal proximity and structure in polyploid evolution.

An Axiom SNP genotyping array for potato: development, evaluation and applications

The paper develops and validates a high-density SNP array for potato, demonstrating its utility in genetic diversity analysis, GWAS, and genomic prediction.

Genome-wide analysis of social behaviour in context: a meta-regression approach across social domains, reporters and developmental stages

This study uses genome-wide meta-regression to analyze social behavior across different contexts, ages, and reporters, identifying six genetic loci and showing modest heritability.

Chromosome-level phased genome assembly of the Argan tree Sideroxylon spinosum L.

The paper presents a chromosome-level phased genome assembly of the Argan tree using PacBio HiFi and Hi-C data, achieving high completeness and resolving telomere-to-telomere chromosomes.

Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies

This study uses deep learning to predict geographic origins of barley genebank accessions and integrates imputed environmental data into genome-environment association studies, revealing both potential and limitations of this approach.

Beyond genetic indicators: how reproductive mode and hybridization challenge freshwater mussel conservation

The paper assesses genetic diversity and other EBVs in freshwater mussels, finding low effective population sizes, hybridization, and reproductive strategies that increase extinction risks.

Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

This study presents a phased chromosome-level genome assembly of sweetpotato, revealing its origin from a wild tetraploid relative and identifying genetic relationships with other progenitors.

Unlocking the full potential of Oxford Nanopore reads with NOVOLoci

NOVOLoci improves genome assembly using Oxford Nanopore reads, achieving high-quality phased assemblies for complex and non-model organisms.

Deep Generative Models for Discrete Genotype Simulation

This study evaluates deep generative models for simulating discrete genotype data, showing their ability to capture genetic patterns and preserve genotype-phenotype associations.

Oatk: a de novo assembly tool for complex plant organelle genomes

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

Pangenome-guided sequence assembly via binary optimisation

This paper introduces a pangenome-guided sequence assembly framework that reduces contigs in complex regions using graph traversal optimisation, with potential for quantum computing implementation.

MULTICLUST - Fast multinomial clustering of multiallelic genotypes to infer genetic population structure

The paper introduces MULTICLUST, a fast maximum likelihood method for clustering multiallelic genotypes to infer genetic population structure, showing comparable accuracy and efficiency to existing methods.

A compact vector for scarless gene editing in E. coli

The paper introduces pCASKD, a single-plasmid system for scarless gene editing in E. coli, demonstrating efficient knock-in and knock-out edits with reduced false positives and faster workflow.

Chromosome-Scale, Telomere-to-Telomere Assembly of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Genome Reveals Lipid Biosynthetic Hotspots and Gene Family Dynamics

The paper presents a high-quality, chromosome-scale genome assembly of the winged bean, identifying lipid biosynthesis hotspots and gene family dynamics.

A platform for the systematic interrogation of genetic interactions in human cells: 26 gene by genome-wide double knockout screens as a proof of concept

The paper introduces a method for systematically studying genetic interactions in human cells using CRISPR/Cas9 screens and demonstrates its effectiveness through 26 gene by genome-wide knockout screens.

Expanding the Egbenema Horizon: Novel Species Discovery in India and First Complete Genome Assembly of the Genus

This study identifies a new cyanobacterial species, Egbenema bharatensis, from India and presents the first complete genome assembly of the genus, highlighting its metabolic versatility and biotechnological potential.

NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

NewtCap is a target capture method for Salamandridae genomes, effective across multiple lineages but not other salamander families, enabling phylogenomics and conservation studies.

Genome report: chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae)

The paper presents chromosome-scale genome assemblies for the olive fruit fly and its symbiont, providing foundational resources for genetic research.

AVITI library prep miniaturization and combining with Illumina data for phylogenomic and population genomic analyses

The paper tests AVITI library prep miniaturization and compares its performance with Illumina for phylogenomic and population genomic analyses, finding high congruence but some issues with miniaturized data.

Genomic Diversity and Population Structure of Red Steppe Cattle Based on High-Density SNP Genotyping

This study genotypes Red Steppe cattle to assess genetic diversity, inbreeding, and population structure using SNP data, identifying three ancestral components and candidates for breeding.

Accurate human genome analysis with Element Avidity sequencing

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

This study identifies Starship transposons as abundant and virulence-associated elements in Verticillium dahliae, showing their role in horizontal gene transfer and virulence evolution.