genome assembly

Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae)

The paper presents chromosome-length genome assemblies for three marten subspecies, revealing genomic features and improving taxonomic understanding.

Improved Genome Assembly of Onygena corvina, a Keratin-Degrading Fungus

This paper improves the genome assembly of Onygena corvina using a hybrid sequencing approach, resulting in a more complete and contiguous genome with enhanced gene annotations.

Multi-locus phylogenetic network analysis of Ampelomyces mycoparasites isolated from diverse powdery mildews in Australia and the generation of two de novo genome assemblies

The paper isolates and analyzes 20 new Ampelomyces strains from Australian powdery mildews, revealing four molecular taxonomic units and generating two high-quality genome assemblies.

Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing

This paper introduces DAF-seq, a method for single-molecule and single-cell chromatin fiber sequencing, enabling precise analysis of protein occupancy and chromatin accessibility.

Discovery of a Novel Chimeric Transposase-Transposon System for Advanced Genome Engineering

The paper identifies and optimizes a novel chimeric transposase system from pea aphids, enhancing transposition efficiency in mammalian cells for improved biologics manufacturing.

Whole-genome resequencing reveals exceptions to panmixia in the exploited top fish predator Antarctic toothfish (Dissostichus mawsoni)

The paper uses whole-genome resequencing to analyze population structure and diversity in Antarctic toothfish, finding exceptions to panmixia and reduced diversity in the Ross Sea post-2000.

High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

The paper presents a high-quality reference genome and genetic map of Allium porrum, revealing pericentromeric recombination patterns and genomic relationships within the Allium genus.

Immortalization of human nasal and bronchial airway epithelial cells for genome editing applications

The paper describes the immortalization of human nasal and bronchial airway epithelial cells using hTERT overexpression, enabling long-term genome editing studies.

Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

This study determines the optimal SNP density for maximizing genomic prediction accuracy and heritability estimates in three spruce species, finding plateaus between 4000 to 8000 SNPs.

A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros)

The paper presents the first reference genome of the Black Redstart, assembled using PacBio HiFi sequencing and annotated with 18,609 genes, providing a resource for studying high-altitude adaptation in passerines.

Whole genome assembly and annotation of the Bumblebee Wax Moth, Aphomia sociella

This paper presents a high-quality genome assembly and annotation for the bumble bee wax moth, Aphomia sociella, using long-read sequencing, and places it phylogenetically within the Lepidoptera order.

Chromosome-Level Genome Assembly of Southern Africa Mozambique Tilapia (Oreochromis mossambicus) using PacBio HiFi and Omni-C sequencing

This paper presents a chromosome-level genome assembly for Mozambique tilapia using PacBio HiFi and Omni-C sequencing, providing a resource for conservation and aquaculture.

ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

The paper presents the chromosome-level genome assembly of Androsace saussurei, a plant adapted to extreme alpine environments.

Do DNA and cytometric measures agree on genome sizes?

This paper compares DNA shotgun read measurements and cytometric genome size estimates across species, finding discrepancies and highlighting the need for better measurement controls.

Palaeogenomics reveals 1,500 years of population history of the peoples of the Chonos Archipelago, Chile.

This study uses paleogenomics to analyze 20 ancient individuals from the Chonos Archipelago, revealing unique genetic clusters and connections to neighboring Indigenous groups.

Targeted sequencing and iterative assembly of near-complete genomes

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

High-quality genome assembly and functional annotation of Hiroshima-derived Pacific oyster Magallana gigas

The paper presents a high-quality genome assembly and functional annotation of Hiroshima-derived Pacific oyster Magallana gigas, providing a genomic resource for studying genetic diversity and environmental adaptations.

Population genetics of the endangered narrowly endemic Island Marble butterfly (Euchloe ausonides insulanus)

This study analyzes the population genetics of the endangered Island Marble butterfly using non-invasive DNA samples to assess genetic diversity, structure, and evolutionary history.

KegAlign: Optimizing pairwise alignments with diagonal partitioning

KegAlign improves pairwise genome alignment speed using GPU acceleration and diagonal partitioning, achieving 150x faster alignment than lastZ for human/mouse genomes.

Complete de novo assembly and re-annotation of the zebrafish genome

The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.

Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome

The paper presents KOREF1-G-TTAGGA, a high-quality telomere-to-telomere Korean reference genome with haplotype-resolved sequences and multi-omic data for precision medicine.

High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus

The paper reports the assembly of 152 high-quality bacterial genomes from the Lotus japonicus root commensal collection using long-read sequencing.

Morphological Variation and DUS Characterization in Bitter Gourd (Momordica charantia L.) collections from Eastern India for Varietal Identification and Genetic Improvement

This study characterizes morphological variation and DUS traits in Bitter Gourd varieties from Eastern India to aid in varietal identification and genetic improvement.

Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus).

The paper presents a genome assembly for white sturgeon and identifies genetic markers for sex determination, aiding conservation and aquaculture efforts.

Multiomic insights into sucrose accumulation in sugarcane

This study uses multiomic approaches to identify genetic variants and genes associated with sucrose accumulation in sugarcane, providing insights for breeding and biotechnology.

Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes

Bin Chicken improves genome recovery from metagenomes by coassembling targeted samples, recovering 77,562 microbial genomes including many novel species.

De novo genome assembly of Ansell's mole-rat (Fukomys anselli)

The paper presents a high-quality de novo genome assembly of Ansells mole-rat using long-read, short-read, and Hi-C data, enabling genetic and phylogenetic studies.

Functional genomics in a microbe that degrades and metabolizes PET plastic

This study develops genetic tools for Piscinibacter sakaiensis to enable functional genomics and engineering for PET degradation.

Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

The paper analyzes the global genomic diversity of C. neoformans over three decades, identifying key genetic features, lineage divergence, and resistance mechanisms.

pGGTOX: a versatile plasmid platform for recombination-based genome editing across Enterobacteriaceae

pGGTOX enables efficient, marker-free genome editing across Enterobacteriaceae using homologous recombination, with applications in gene deletion, plasmid modification, and CRISPR delivery.