genome assembly

Genome-wide SNP diversity in natural and cultivated populations informs restoration ecology with three Calamagrostis species from the Northwest Territories of Canada

The paper uses ddRAD and GT-seq to analyze genetic diversity in three Calamagrostis species, informing seed sourcing strategies for restoration in northern Canada.

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction

The paper presents chromosome-scale genome assemblies of four duckweed species, revealing genomic plasticity and adaptations to aquatic environments through gene loss and pathway retention.

High-throughput DNA engineering by mating bacteria

This paper introduces SCRIVENER, a bacterial mating-based DNA assembly platform that enables high-throughput, low-error DNA construction of up to 23 kb constructs.

Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis

The paper presents a chromosome-scale genome assembly of Halocafeteria seosinensis using long-read sequencing, enabling detailed genomic analysis of a halophilic protist.

Genome-wide absolute quantification of chromatin looping

This study calibrates Micro-C with live imaging to determine absolute chromatin looping probabilities in mouse cells, finding most loops occur at low frequencies.

A high-quality genome resource for Cercospora cf. flagellaris, a causal agent of Cercospora leaf blight of soybeans

The paper presents a high-quality genome assembly of Cercospora cf. flagellaris, identifying genes and pathways relevant to its pathogenicity and host interactions.

Assembly of a high-quality reference genome for the rat tapeworm Hymenolepis diminuta

The paper presents a high-quality reference genome for Hymenolepis diminuta using PacBio HiFi long-read sequencing, achieving high contiguity and completeness.

Genomic predictions of climate change vulnerability in the emblematic mountain butterfly Parnassius apollo

This study uses genomic data to predict climate change vulnerability in the Apollo butterfly, identifying populations at varying risk based on genetic diversity and adaptation potential.

A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing

De novo genome assemblies of threatened Asian hornbills (Bucerotidae) reveal declining population trajectories during the late Pleistocene

This study presents de novo genome assemblies for four Asian hornbill species and estimates their Pleistocene population declines due to climate fluctuations.

Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array

This study develops a 72k SNP array to assess BKD resistance in Arctic charr and finds genomic prediction is feasible with moderate accuracy.

TandemTwister: Scalable genotyping and advanced visualization of tandem repeats

TandemTwister is a tool for tandem repeat genotyping and visualization, showing high accuracy and speed across sequencing technologies and datasets.

Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes

This paper introduces a method for efficient, single-step genome editing of bacteriophages using targeted DNA nicking, achieving high recombination rates without reducing phage titers.

A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

The paper presents a high-quality, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei using long-read and Hi-C sequencing.

A chromosome-level reference genome for the colonial marine hydrozoan Podocoryna americana

This paper presents a chromosome-level genome assembly for Podocoryna americana, revealing gene family expansions and contractions compared to other cnidarians.

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

SPA-C improves genome scaffolding by combining Hi-C data with a CNN and graph-solving algorithm, outperforming existing methods on benchmark genomes.

Identification of heterotic group-specific haplotypes and impact of residual inbreeding on grain yield of maize elite hybrids

This study identifies heterotic group-specific haplotypes and shows that residual inbreeding from commercial hybrids negatively impacts maize grain yield.

Genetic mapping and nuclear interactions of an incompatibility response in Agaricus bisporus

The paper maps incompatibility alleles in Agaricus bisporus and identifies three chromosomal loci associated with mycelial compatibility.

The first reference genome assembly of the Chilean sea fig (Carpobrotus chilensis)

The paper presents a draft genome assembly of Carpobrotus chilensis, revealing low heterozygosity, high transposable element content, and low sequence divergence from its invasive relative C. edulis.

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16

The paper presents a gap-free, telomere-to-telomere genome assembly for the C. briggsae AF16 strain, along with improved gene annotations and variant mappings.

Insights from farming Macrocystis pyrifera offshore: phenotypic analysis, genome-wide association studies, genomic selection

The paper analyzes phenotypic data and performs genome-wide association studies and genomic selection for giant kelp to improve breeding programs.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata

This paper presents a high-quality chromosome-scale genome assembly of Oryza granulata, a shade-tolerant wild rice, using PacBio, Hi-C, and Illumina sequencing.

De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

The paper presents de novo genome assemblies of four rainbow trout lines to identify structural variants and build a pangenome reference for studying domestication and adaptation.

GnnDebugger: GNN based error correction in De Bruijn Graphs

GnnDebugger uses Graph Neural Networks to correct errors in De Bruijn Graphs, improving genome assembly accuracy for diploid genomes with low coverage.

First report of genetic transformation and CRISPR/Cas12a-mediated gene editing of European beech (Fagus sylvatica L.) employing a transient protoplast system

This paper establishes a transient protoplast system for genetic transformation and CRISPR/Cas12a-mediated gene editing in European beech, achieving editing efficiencies in the PHYTOENE DESATURASE gene.

Genome reorganization and its functional impact during breast cancer progression

The paper profiles genome organization changes during breast cancer progression using Micro-C mapping and links these changes to gene expression and enhancer activity.

Long-read single-cell genomics: resolving chimeras in multiple displacement amplification

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

Chromosome-level genome assembly of the Northeast China Brown Frog (Rana dybowskii)

The paper presents a chromosome-level genome assembly for Rana dybowskii using PacBio HiFi and CiFi, achieving high completeness and gene prediction.