genome assembly

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Creation of genomic chimeras via megabase scale genome expansion

This paper introduces ACE, a method to create genomic chimeras by integrating large genomic segments from donor cells into a recipient genome, demonstrating its ability to generate stable chimeric organisms across species barriers.

WheatPanRef: a unified linear pan-reference genome for wheat genomics

WheatPanRef provides a unified linear pan-reference genome for wheat, improving read alignment and enabling integration of genomic resources across diverse accessions.

Genomic prediction of resistance to Phytophthora megakarya in cacao from a sparse host-pathogen screen

This study predicts cacao resistance to Phytophthora megakarya using genomic data, finding that host genomic relationships are more predictive than pathogen relatedness in a structured host-pathogen system.

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

De novo genome assembly of the floating-hook moss Warnstorfia fluitans

This paper presents the first de novo genome assembly of the floating-hook moss Warnstorfia fluitans, along with its chloroplast and mitochondrial genomes, providing a resource for ecological and evolutionary studies.

Four genome assemblies of new wild Gossypium hirsutum accessions from the Yucatan Peninsula, the center of domestication

The paper reports four new chromosome-level genome assemblies of wild Gossypium hirsutum from Yucatan, highlighting their genetic diversity and potential for improving cotton resistance traits.

GENOME ASSEMBLIES FOR 28 PHAEOSPHAERIACEAE ISOLATES FROM CANADA

The paper reports whole genome assemblies of 28 Phaeosphaeriaceae isolates from Canada, revealing genetic diversity and potential new species.

Bone Response to Mechanical Loading is Highly Heritable and Correlates with Osteocyte Lacunar Morphology in Genetically Diverse Mouse Strains

This study shows that genetic background strongly influences bone response to mechanical loading in mice, with high heritability and correlations with osteocyte lacunar morphology.

A Chromosome Scale Genome Assembly for the Australian blue mussel Mytilus planulatus

The paper presents the first chromosome-scale reference genome for Mytilus planulatus, revealing structural variation and population structure in mussels.

Cell-in-drop genotyping detects megabase-scale loss of heterozygosity as a quantitative marker for CRISPR-Cas9 on-target toxicity

X-Chromosomal STR-based analysis of genetic diversity, structure, and phylogeny in the Sri Lankan Vedda population

This study analyzes X-chromosomal STR diversity in the Vedda population, finding significant genetic differentiation from other South Asian groups and highlighting their unique genetic heritage.

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

This paper presents the first high-quality genome assembly of a cave-dwelling remipede, revealing a repeat-rich genome with extensive gene family turnover and phylogenetic signals.

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

The paper tests if climate-associated genomic variation predicts phenotypic adaptation in European wild apple, finding genomic offsets link to bud-break timing but not other traits.

Complete genome sequence and metabolic features of Vreelandella zhaodongensis BS253: A new isolate from hypersaline lakes from Brazilian Pantanal

This paper reports the complete genome sequence and metabolic features of a new extremophile isolate, Vreelandella zhaodongensis BS253, from a hypersaline lake, highlighting its potential for biotechnological applications in carbon capture and sustainable processes.

A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

Asymmetric migration shapes genetic structure of the invasive avian vampire fly (Philornis downsi) across the Galapagos Islands.

This study investigates the genetic structure and dispersal patterns of Philornis downsi across Galapagos Islands using whole genome sequencing, finding asymmetric gene flow and genetic divergence linked to trade winds and shipping routes.

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

A synthetic genetic switch for tracking T-DNA delivery supports integration-free genome editing in plants

The paper develops T-SWITCH, a synthetic genetic switch that tracks T-DNA delivery and integration in plants, enabling integration-free genome editing.

Towards a complete diploid chicken genome

This paper presents a nearly complete haplotype-resolved chicken genome using trio-sequencing and long-read data, identifying gaps and structural variants in dot chromosomes.

A chromosome-level genome assembly of the classical model nematode Panagrellus redivivus for comparative studies of parasitism evolution

The paper presents a chromosome-level genome assembly of Panagrellus redivivus, enabling comparative studies of parasitism evolution by providing a non-parasitic reference genome.

A haplotype-resolved, near telomere-to-telomere genome assembly of the desiccation-tolerant plant Vellozia tubiflora

This paper presents a near telomere-to-telomere, haplotype-resolved genome assembly of Vellozia tubiflora, a desiccation-tolerant plant, providing genomic resources for evolutionary and comparative studies.

Manta and devil ray genome assemblies uncover signatures of pelagic adaptation

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

This study presents a chromosome-scale genome assembly of Edelweiss, revealing its recent allotetraploid origin and localized subgenome dominance.

Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii

This paper develops a CRISPR-Cas9 system for Anaerocellum bescii, enabling gene deletions and vector maintenance through thermostable Cas9.

Rescued from extinction in two buckets: genomic consequences of an extreme bottleneck in the endangered Owens pupfish

The paper analyzes the genomic consequences of a severe bottleneck in Owens pupfish, finding reduced genetic diversity and a 17-fold contraction in effective population size, but low recent inbreeding due to population expansion.

Reaction Norm Modeling of High-Dimensional Genomic and Environmental Data Improves Prediction Accuracy in Winter Wheat

This paper improves genomic prediction accuracy in winter wheat by integrating genotype-by-environment interactions and environmental covariates across multiple environments.

Genome and methylome of the root crop table beet (Beta vulgaris)

The paper presents a chromosome-scale genome and methylome assembly for table beet, identifies candidate genes for geosmin production, and compares it with sugar beet.

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

This paper presents a chromosome-scale genome assembly for rubber dandelion, identifies key rubber pathway genes, and links chromosome reorganization to domestication traits.