genome assembly

Genome assembly of Spinifex sericeus provides insights into repetitive content and haplotype variation in a dioecious coastal grass

This paper presents a near telomere-to-telomere, haplotype-resolved genome of Spinifex sericeus, revealing structural variation and repetitive content that may drive genome evolution.

BayesR3AD: Joint analysis of additive and dominance in Bayesian mixture models

BayesR3AD extends Bayesian mixture models to jointly estimate additive and dominance genetic effects, improving prediction accuracy for fertility and longevity in Holstein cattle.

A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

The paper presents a chromosome-level genome assembly and functional genomic resources for Capitella teleta, improving upon an outdated reference and enabling better analysis of multi-omic data.

Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource

The paper develops and validates a mid-density SNP array for sorghum using NGS, showing it performs as well as high-density GBS for trait prediction and breeding applications.

A new-engineered integrative tool to target the terminal compartment of the Streptomyces chromosome

This paper introduces a new integrative tool, Samy, for targeting the terminal compartment of Streptomyces chromosomes, expanding genetic engineering capabilities.

Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae

The paper validates a method to generate genome-wide polymorphism datasets from individual hookworm larvae, showing that accurate variant calling is possible with sufficient DNA input and strict filtering.

High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB

Tobacco rattle virus delivery of engineered ISDra2 variant eTnpBc and its guide RNA as a single transcript achieves up to 90% somatic and 100% heritable editing in Nicotiana benthamiana.

Distinct genetic profiles influence body mass index between infancy and adolescence

This study identifies age-varying genetic contributions to BMI using longitudinal data from the ALSPAC cohort, showing distinct genetic profiles in infancy versus later childhood and adolescence.

Genomes of the Golden Horde Elites and their Implications for the Rulers of the Mongol Empire

The paper analyzes the genomes of Golden Horde elites to confirm Genghis Khan's Y-chromosome haplogroup and trace their genetic ancestry.

First haplotype-resolved genome assembly of citral-rich lemongrass Cymbopogon flexuosus var. Krishna

The paper presents the first haplotype-resolved genome assembly of lemongrass, providing a high-quality reference for genetic and metabolic studies.

Transient telomere uncapping triggers telomeric and subtelomeric rearrangements

This study shows that transient telomere uncapping in yeast causes genomic rearrangements and telomere elongation, with implications for genome stability and evolution.

The genome sequence of Pavonine herpesvirus 1, a novel Mardivirus infecting peafowl

This paper reports the genome of Pavonine herpesvirus 1, a novel Mardivirus from peafowl, showing it lacks oncogenic genes found in Mareks disease virus.

A Tissue Culture Free Genome Editing Strategy in Plants Using Broad-Host-Range Viral Vectors Derived from Geminiviruses

This paper develops a tissue culture-free genome editing system in plants using geminivirus vectors, achieving efficient Cas9, Cas12f, and Cas12j expression with reduced cargo size.

PyMSQ: a python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection

PyMSQ provides a fast Python package for computing Mendelian sampling variance, covariance, and haplotype-based similarity in genomic selection, enhancing haplotype diversity management.

T2T genomes of Caenorhabditis nigoni and Caenorhabditis briggsae reveals extensive loss of satellite DNA associated with self-fertilization

The paper compares T2T genomes of C. nigoni and C. briggsae, finding that self-fertilization is associated with loss of satellite DNA, particularly on the X chromosome.

Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae)

This paper presents a high-quality chromosome-scale genome assembly for Gryllus bimaculatus using long-read sequencing and Hi-C data, significantly improving contiguity and gene annotation completeness.

QTL mapping, breeding, and debugging Saccharomyces cerevisiae strains through Reiterated Mass Selection and backcrosSing (ReMaSSing)

This paper introduces ReMaSSing, a method to identify and correct adaptive alleles in Saccharomyces cerevisiae for improved lignocellulosic hydrolysate tolerance through QTL mapping and breeding.

A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species

This paper presents a chromosome-level genome assembly of Urochloa humidicola, revealing its octoploid structure, evolutionary origins, and subgenome relationships.

Transposable elements hitchhike on Starships across fungal genomes

The paper identifies Starships as vectors for horizontal transfer of transposable elements (TEs) in fungi, showing their role in TE bursts and genome structural changes.

Graph pangenome reveals structural variation dynamics during cucumber breeding

The paper constructs a cucumber pangenome to analyze structural variant dynamics during domestication and breeding, finding SVs are purged more than SNPs and improving genomic prediction accuracy.

DNA polymerase kappa stabilized by PTBP2 interacts with MRE11 and promotes genomic instability in leukemia cells

The paper shows PTBP2 stabilizes Pol{kappa} mRNA, leading to genomic instability in CML cells by interacting with MRE11 and promoting DNA damage.

Reference genome choice impacts SNP recovery but not evolutionary inference in young species

This study evaluates how reference genome choice affects RAD-seq analyses in Petunia and Calibrachoa, finding that closely related genomes yield consistent results while distantly related ones reduce SNP recovery but not evolutionary inference.

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

This study uses non-invasive genomic sampling to analyze genetic diversity in wild gorillas, revealing population clusters and migration patterns, and predicts geographic origins with high accuracy.

From Diversity to Discovery: Genome-Wide Insights into the Genetic Landscape of Tropical Maize DH Lines

The paper analyzes genetic diversity and population structure in 2,555 tropical maize DH lines using SNP markers, revealing two major genetic clusters and high within-group diversity for genomic studies.

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

The paper presents the first chromosome-level genome assembly of Flustra foliacea and identifies chromosomal fusions and retrotransposon enrichment in its genome.

Genome sequencing, de novo assembly and annotation of the commercially important bamboo, Bambusa tulda Roxb.

The paper reports the genome sequencing, de novo assembly, and annotation of Bambusa tulda, providing a high-quality draft genome for future research.

The historical patterns that have shaped contemporary genetic differentiation across populations of Arctic charr in Scotland

This study examines genetic differentiation in Arctic charr across Scotland, finding that glacial history influenced colonization and genetic patterns despite geographic distance.

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

The paper introduces hifiasm (ONT), an algorithm that enables near telomere-to-telomere genome assembly using standard ONT Simplex reads, reducing computational demands and improving chromosome reconstruction.

The genetic architecture of local adaptation is historically contingent

This study uses simulations to show how ecological and genetic factors shape the genetic architecture of local adaptation, highlighting the role of demographic history and allele age in genotype-environmental associations.

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

The paper presents a chromosome-scale, haplotype-resolved genome assembly for Quercus virginiana, contributing to genomic resources for studying hybridization and structural genomic changes in oaks.