genome assembly

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences

BINSEQ introduces binary formats for sequencing data to enable faster parallel processing, reducing analysis time for genome and transcriptome studies.

The Il1r2-CreERT2 knock-in mouse enables inducible labeling of slow-cycling epidermal basal cells and genetic ablation of the IL-1 decoy receptor

This study identifies Il1r2 as a marker for slow-cycling epidermal basal cells and develops a genetic tool for lineage tracing and IL-1 signaling modulation.

A draft de novo assembly of Diadema antillarum, a keystone herbivore of the Caribbean reefs

This paper presents a high-quality de novo genome assembly of Diadema antillarum using multiple sequencing platforms and assembly strategies.

Pharmacological stress exposes hidden allelic background effects in genetic interaction screen normalisation

The paper shows that pharmacological stress reveals hidden allelic background effects in genetic interaction screens, using fission yeast and Torin1 to demonstrate divergent fitness profiles.

Closely related, yet phenotypically different - Genome assemblies of two sister species of widow spiders: Latrodectus hasselti and L. katipo, Theridiidae

The paper presents genome assemblies for two closely related widow spider species, L. hasselti and L. katipo, and reports their gene content and repeat composition.

Read-Consistent Minimum Unique Substrings: A Parameter-Free, Linear-Time Framework for Genomic Sequence Representation

This paper introduces Minimum Unique Substrings (MUSs) as a parameter-free, linear-time framework for genomic sequence representation, showing improved coverage and resolution compared to fixed-length k-mers.

Efficient and accurate near telomere-to-telomere haplotype reconstruction of diploid genomes

HapFold improves haplotype reconstruction for diploid genomes by combining graph-based and sequence-based scaffolding methods, achieving high accuracy and contiguity.

Clinical Campylobacter jejuni isolates: genomes and genetic tools

The paper sequences two Campylobacter jejuni strains and develops a plasmid system to enhance genetic tools for studying clinical isolates.

Census and genetic analysis of the United States marmoset population

The paper analyzes the genetic diversity and population structure of US marmosets, revealing pre-colony population structure and generating a pedigree-based recombination map.

DeepBioGS: a hybrid framework for integrating crop growth modelling with genomic prediction through neural networks

DeepBioGS integrates genomic selection with crop growth models using deep learning to improve prediction of genotype performance across environments.

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

This paper presents the first chromosome-scale, haplotype-resolved genome assembly and annotation for Carya glabra, revealing it as an autotetraploid and providing resources for ecological and agricultural studies.

Telomere-to-telomere, accurate, and gapless genome assembly (TTAGGA) of the Korean Jindo dog with a single-contig Y chromosome

The paper presents a gapless, haplotype-resolved canine genome assembly for a Jindo dog, achieving high completeness and accuracy for the Y chromosome.

Interplay between purging and admixture shapes genetic load in an invasive guppy population

The paper examines how purging and admixture affect genetic load in an invasive guppy population, finding that strongly and weakly deleterious mutations respond differently to these processes.

The high-quality genome assembly of Coelioxoides waltheriae (Apidae: Nomadinae) reveals gene family dynamics and evolutionary shifts related to its cleptoparasitic lifestyle

This paper presents the first high-quality genome assembly of a cleptoparasitic bee, revealing gene family contractions and expansions linked to its parasitic lifestyle.

Near chromosome-level genome assembly for the invasive annual forb Centaurea melitensis

The paper presents a near chromosome-level genome assembly for Centaurea melitensis, revealing structural variation and gene content.

A chromosome-level reference genome for Pacific herring (Clupea pallasii) from the Bering Sea

The paper presents a chromosome-level reference genome for Pacific herring from the Bering Sea, improving genomic resources for this species.

Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

The paper presents a chromosome-scale genome assembly of the common cuttlefish Sepia officinalis, revealing its true karyotype and identifying cephalopod-specific gene expansions.

Selection For Yield Enhanced Rhizobial Mutualism In Pea

The paper investigates the genetic correlation between yield and rhizobial mutualism traits in pea cultivars and wild accessions, finding a positive correlation that suggests yield selection maintains or enhances mutualism benefits.

Water Stress Tolerance, Genomic Selection and Identification of Genomic Regions in a MAGIC Population of Eggplant

The paper evaluates water stress tolerance in eggplant MAGIC lines, identifies genomic regions associated with stress traits, and develops a genomic selection index to predict stress tolerance.

Chromosome-level genome assemblies of the red algae Porphyra dioica and Porphyra linearis

The paper presents chromosome-level genome assemblies for two red algae species, providing a framework for comparative studies and selective breeding in aquaculture.

Chromosome-level genome assembly and annotation of the threatened marbled teal (Marmaronetta angustirostris)

The paper presents the first chromosome-level genome assembly for the marbled teal, enabling analyses of inbreeding and genetic variation in this threatened species.

New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)

The paper presents new chromosome-level haplotyped genome assemblies for the Japanese quail, improving contiguity and completeness compared to previous references.

First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America

This paper generates genome-wide data from pre-Ceramic Caribbean individuals, showing genetic continuity with Central America and northern South America and small, locally structured communities.

Linear plasmid prevalence and linezolid resistance gene carriage in vancomycin-resistant Enterococcus in Canada from 2009-2024

This study examines the prevalence of linear plasmids and linezolid resistance genes in vancomycin-resistant Enterococcus isolates in Canada from 2009 to 2024, finding increasing plasmid carriage and co-localization of resistance genes.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The Revised Diploid Genome Sequence of an Individual Human: An Optimized Assembly Workflow for Scaling of near Telomere-to-Telomere Assemblies

The paper revises a human diploid genome assembly using a scalable workflow with Oxford Nanopore reads, achieving high accuracy and contiguity without ultra-long reads or other technologies.

Genomic prediction of single cross families of perennial ryegrass in two nitrogen managements

This study predicts single cross performance in perennial ryegrass using genomic models, finding high predictive accuracy for dry matter yield and nutritive quality traits.

16p11.2 Copy Number Variation Alters Genome Architecture and Transcriptional Regulation During Neurodevelopment

This study investigates how 16p11.2 copy number variations affect genome architecture and transcription during neurodevelopment, finding both local dosage effects and broader chromatin changes.

Eleven deep-sea coral genome assemblies unveil insights into evolution, adaptation, and coral biodiversity

The paper presents 11 deep-sea coral genome assemblies, revealing evolutionary dynamics, environmental adaptation, and genetic differences between deep-sea and shallow-sea corals.

Genome Assembly of Astatotilapia latifasciata Uncovers B Chromosome Linked Chromatin Reorganization

The paper presents a chromosome-level genome assembly of Astatotilapia latifasciata, revealing a B chromosome with unique gene content and chromatin structure.