genome assembly

The genomic outcomes of hybridization vary over time within a monkeyflower radiation

This study examines how hybridization impacts genomes at different stages of speciation in monkeyflowers, finding that selection against recent introgression is stronger than against ancient introgression.

Oryza genome evolution through a tetraploid lens

The paper presents 11 new chromosome-level genome assemblies of Oryza species, revealing core genome conservation and subgenome plasticity, and highlights implications for crop improvement.

Genetic differentiation in Anopheles stephensi from India and Ethiopia: insights from mitochondrial genome analysis

This study analyzes mitochondrial genomes of Anopheles stephensi from India and Ethiopia to reveal genetic differentiation and multiple lineages, suggesting independent introductions.

Genetic differentiation and adaptive evolution of buff-tailed bumblebees in Asia

The paper analyzes genetic differentiation and adaptive evolution of buff-tailed bumblebees in Asia and Europe, identifying genetic markers associated with environmental adaptation.

Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies

The paper evaluates CycloneSEQ long-read sequencing for improving bacterial genome assemblies, showing it can produce complete circular genomes when combined with short-read data.

Three annotated chromosome-level de novo genome assemblies of Lomentospora prolificans provide evidence for a chromosomal translocation event

This study presents three chromosome-level genome assemblies of Lomentospora prolificans, revealing a chromosomal translocation event between strains.

Make-or-break prime editing for bacterial genome engineering

This paper develops mbPE, a prime editing system for Streptococcus pneumoniae that enables precise genome editing without donor DNA, achieving high selection efficiencies for point mutations, deletions, and insertions.

Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis

This paper engineers a plant virus to deliver a compact CRISPR-Cas system for transgene-free germline editing in Arabidopsis.

Electrical charge-mediated transformation for efficient plant genome editing

This paper introduces an electric charge-mediated method for efficient plant genome editing in faba bean, achieving 50% mutation success rate in the PDS gene without DNA vectors.

Reference-guided genome assembly at scale using ultra-low-coverage high-fidelity long-reads with HiFiCCL

HiFiCCL improves ultra-low-coverage genome assembly using high-fidelity long-reads, enhancing structural variant detection and pangenome construction in human and plant datasets.

P53 deficiency triggers hypertranscription, inducing nucleotide insufficiency causing replication stress, and genomic instability

This study shows that p53 deficiency causes hypertranscription and nucleotide insufficiency, leading to replication stress and genomic instability, including chromothripsis.

The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12

The paper reports a high-quality haplotype-resolved genome assembly of a cassava line resistant to cassava brown streak disease, revealing structural variations linked to resistance.

Back to the Future: Environmental genomic selection to take advantage of polygenic local adaptation

This paper applies environmental genomic selection to barley landraces to identify key parents for breeding adapted to specific environments.

Disparate co-evolution and prevalence of sulfadoxine and pyrimethamine resistance alleles and haplotypes at dhfr and dhps genes across Africa

The paper analyzes the evolution and prevalence of dhfr and dhps resistance alleles and haplotypes across Africa using whole genome data from multiple countries.

A phased chromosome-level genome of the annelid tubeworm Galeolaria caespitosa

The paper presents the first phased, chromosome-level genome of the annelid tubeworm Galeolaria caespitosa, revealing chromosomal rearrangements and gene annotations.

Laboratory evolution of the bacterial genome structure through insertion sequence activation

This study accelerates bacterial genome evolution by introducing multiple insertion sequences into E. coli, resulting in significant genome rearrangements and size changes.

Resource presentation dictates genetic and phenotypic adaptation in yeast.

This study shows that subtle environmental changes in sugar presentation alter genetic and phenotypic adaptation in yeast, with predictable pleiotropic effects.

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly

Colora provides a Snakemake workflow for automated, high-quality chromosome-scale de novo genome assembly using PacBio HiFi, Hi-C, and optionally ONT reads.

Genomic data reveal a north-south split and introgression history of blood fluke (Schistosoma haematobium) populations from across Africa

The paper analyzes genomic data from Schistosoma haematobium populations across Africa, revealing a north-south genetic split and ancient introgression events with S. bovis, with some genes approaching fixation and sex chromosomes showing introgression resistance.

Chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris (Stylommatophora: Camaenidae)

This paper presents a chromosome-level genome assembly and transcriptome for Bradybaena similaris, a terrestrial snail in the superfamily Helicoidea, enhancing genomic resources for evolutionary studies.

Genome-wide differentiation and SNP-based identification of northeastern Atlantic Sebastes species

The paper identifies genetic differentiation and develops SNP markers for distinguishing Sebastes species in the northeastern Atlantic, revealing cryptic species and ecotypes.

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

The genome assembly of the duckweed fern, Azolla caroliniana

The paper presents a chromosome-level genome assembly of Azolla caroliniana, improving upon previous assemblies and aiding in understanding its population genetics and taxonomy.

Eukfinder: a pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data.

Eukfinder is a pipeline that recovers high-quality eukaryotic microbial genomes from metagenomic data, outperforming existing tools in assembling near-complete genomes without a reference.

Blood pressure, cardiometabolic traits and cardiovascular events in women with uterine fibroids: a genetic correlation and Mendelian randomization study

This study investigates genetic correlations and causal relationships between uterine fibroids and cardiometabolic traits using genetic data and Mendelian randomization.

Genome assembly and annotation of Acropora pulchra from Mo'orea French Polynesia

The paper presents the genome and DNA methylome assembly of Acropora pulchra from Moorea, French Polynesia, achieving high completeness and providing insights into its genetic and epigenetic features.

Recent emergence of cephalosporin resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene

Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence

This study identifies the genetic basis of silver iridescence polymorphism in Mormon Fritillary butterflies, linking it to the optix gene and showing evidence of selection and introgression.

Complete sequencing of ape genomes

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

Optimized vectors for genetic engineering of Aureobasidium pullulans

The paper designs and tests 25 optimized vectors for genetic engineering of Aureobasidium pullulans, enabling dual protein expression and homology-based gene modification.