genome assembly

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

The paper presents a pseudo-phased genome assembly of H. vastatrix isolate Hv178a, revealing a chromosomal trisomy of chr17 associated with increased virulence.

Approaching an Error-Free Diploid Human Genome Using a Support-Based Validation Framework

The paper introduces a support-based validation framework to correct assembly errors in diploid genomes using independent sequencing evidence.

Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding

The paper assembles chromosome-scale diploid genomes of prairie and meadow voles using a single-library approach, identifying a prairie-vole-specific duplication of Avpr1a associated with pair bonding.

Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations

The paper analyzes deleterious mutations in cheetah populations, finding higher inbreeding and sperm-related mutation enrichment in certain populations.

Anchors for Homology-Based Scaffolding

This paper introduces an anchor-based scaffolding framework for homology-based ordering of contigs, achieving accuracy comparable to state-of-the-art methods, especially in multi-reference settings.

Rare variants drive high variance in human ancestral fitness at mutation-selection-drift balance

The paper estimates human genetic load variation due to rare and ultra-rare deleterious mutations, showing significant ancestral fitness differences between individuals.

Multiplex genome engineering in yeast using the TIGR-Tas system

This paper demonstrates the use of TIGR-Tas system for multiplex genome engineering in yeast, achieving targeted DNA breaks and gene modifications without PAM requirements.

De novo genome sequence assembly of the model algal endosymbiont Micractinium conductrix derived from its host Paramecium bursaria 186b

The paper reports a near telomere-to-telomere genome assembly of Micractinium conductrix, enabling genomic studies of endosymbiosis and biotechnological applications.

A Saccharomyces cerevisiae Model for Overexpression of Ntg1 a Base Excision DNA Repair Protein Reveals Novel Genetic Interactions

This paper develops a Saccharomyces cerevisiae model to study how overexpression of the BER protein Ntg1 affects cell growth and DNA damage, revealing genetic interactions and regulatory mechanisms.

PlasChain: an algorithm for improving long plasmid reconstruction from metagenome assemblies

PlasChain improves long plasmid reconstruction from metagenome assemblies by addressing fragmentation and false positives, outperforming existing methods in recovering long plasmids.

ImPaqT - A Golden Gate-based Toolkit for Zebrafish Transgenesis

The paper introduces ImPaqT, a Golden Gate-based toolkit for zebrafish transgenesis, enabling rapid and flexible transgene construction and immune reporter line generation.

Genetic engineering of Staphylococcus haemolyticus: Overcoming Restriction-Modification Barriers and Targeting Virulence Genes

This paper develops molecular tools to overcome restriction-modification barriers in Staphylococcus haemolyticus, enabling genome editing and virulence gene targeting.

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

The paper analyzes the genomic diversity of C. tropicalis, finding geographic correlation and hyper-divergent regions linked to environmental adaptation.

The Polyploid History of Cultivated Dahlia

The paper assembles and annotates the genome of a tetraploid Dahlia variabilis cultivar, identifying it as a segmental tetraploid with evidence of auto- and allopolyploidy.

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Inter-haplotype inversions and repeat expansion in the sexually deceptive orchid Chiloglottis trapeziformis

This paper presents the first chromosome-scale, haplotype-resolved nuclear genome assembly for Chiloglottis trapeziformis, revealing structural variation and repeat-rich features.

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

The paper presents a chromosome-level genome assembly of Cupressus sempervirens, revealing insights into conifer genome evolution and the role of transposable elements.

Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species

The paper constructs chromosome-scale genomes for three Cupressaceae species to study chromosomal evolution and speciation, finding chromosomal rearrangements and segmental duplications contributed to species divergence.

Evolutionary dynamics of the Timopheevii wheat lineage

The paper presents genomic resources for the Timopheevii wheat lineage, revealing evolutionary dynamics including homoeologous exchange, genome instability, and geographic range expansion.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Phenotyping replication is a major determinant of genomic predictive ability in sweet sorghum (Sorghum bicolor Moench)

The paper evaluates how phenotyping replication, training population size, and genomic relatedness affect genomic predictive ability in sweet sorghum breeding programs.

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

Genomic diversity of elm trees for future treescapes

The paper analyzes genomic diversity in elm trees to assess the genetic potential of resistant cultivars for restoration.

The Dynamics of Long Terminal Repeat Proliferation in the Hesperis matronalis Genome

This study presents the genome sequence of Hesperis matronalis, revealing the dynamics of LTR retrotransposon proliferation and their role in genome expansion within the Brassicaceae family.

A rhizarian genome reveals an osmotrophic route to extracellular digestion in eukaryotes

The paper presents the first telomere-anchored genome of a rhizarian, revealing an osmotrophic extracellular digestion strategy similar to saprotrophic fungi.

A highly contiguous genome assembly of Cyclamen persicum to accelerate functional genomics and breeding

This paper presents a high-quality genome assembly for Cyclamen persicum, enabling genomic studies and breeding improvements.

Binary node clustering via contrastive learning for haplotype phasing in de novo genome assembly

This paper introduces grapHiC, a contrastive learning framework for reference-free haplotype phasing in de novo genome assembly, achieving results comparable to state-of-the-art methods.

Three annotated tiger beetle genomes (Coleoptera, Adephaga, Cicindelidae)

This paper reports the annotation of three tiger beetle genomes, providing draft reference genomes for evolutionary and conservation studies.

High relatedness in sexually produced restoration cohorts of the endangered elkhorn coral, Acropora palmata

The paper assesses genetic diversity and relatedness in sexually produced coral offspring to inform restoration strategies.