genome assembly

Genetic Dissection of Grain Yield and Correlated Proxy Traits Under Suboptimal Conditions

The paper develops a maize MAGIC population to dissect grain yield and proxy traits under stress, identifying QTL and improving genomic prediction models.

High-Molecular-Weight Genomic DNA Extraction from Recalcitrant Australian Plants: An Optimised CTAB Protocol for Anigozanthos

This paper develops an optimised CTAB protocol for extracting high-molecular-weight DNA from recalcitrant Australian plants, improving DNA purity and integrity for sequencing.

Genomic Architecture of Migraine: A Multi ancestry GWAS Meta analysis of 2.5 Million Participants

This study conducts a multi-ancestry GWAS meta-analysis of 2.5 million participants to identify genetic variants associated with migraine and link them to biological pathways and therapeutic targets.

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome

ECHO is a nanopore sequencing pipeline for comprehensive (epi)genetic analysis of the human repeatome, enabling haplotype-resolved and methylation-informative studies.

Genetic parameters and genotype-by-diet interactions forgrowth traits in Australian black soldier fly larvae: Implicationsfor selective breeding

This study estimates genetic parameters and genotype-by-diet interactions for growth traits in black soldier fly larvae, finding moderate heritability and significant dominance effects.

The first chromosome-scale genome assembly of Blumeria graminis f. sp. avenae provides insights into genome evolution and host specialization

A subgenome-resolved and chromosome-scale reference genome assembly of allotetraploid wheat wild relative Aegilops peregrina

This paper presents a high-quality chromosome-scale reference genome assembly for Aegilops peregrina using PacBio HiFi and Hi-C sequencing, enabling genomic analysis of its subgenomes.

Limited neutral and adaptive genomic divergence suggests Acropora cervicornis can be managed as a single conservation unit across its range

The paper analyzes genomic data from Acropora cervicornis to assess neutral and adaptive divergence, finding limited genetic structure and suggesting it can be managed as a single conservation unit.

A practical sampling strategy for biodiversity genomics of reptiles: The Cryptoblepharus pulcher assembly offers insights into the demise of a threatened relative

The paper evaluates a practical tissue sampling strategy for non-model reptiles, demonstrating that ethanol-preserved samples can yield high-quality genomic data and provide insights into the evolutionary history of a threatened species.

Genome report: Genome sequence of Phymata mystica (Evans), an ambush bug

The paper reports the genome sequence of Phymata mystica, an ambush bug, and identifies conserved venom proteins, providing insights into venom evolution in Heteroptera.

Integrative optical genome mapping and long-read sequencing resolve constitutional complex rearrangements at nucleotide resolution

The paper uses optical genome mapping and long-read sequencing to resolve complex rearrangements at nucleotide resolution, revealing additional complexity and enabling accurate genotype-phenotype correlations.

Genomic status of the Eurasian curlew Numenius arquata : estimating Essential Biodiversity Variables and selection signals for a declining migratory bird

The paper analyzes genomic data from Eurasian curlews to assess genetic diversity, population structure, and selection signals in declining populations.

Highly contiguous reference genome assembly of the endangered Orces blue whiptail Holcosus orcesi

The paper presents a high-quality reference genome for the endangered Orces Blue Whiptail lizard using long-read sequencing, providing a foundation for evolutionary and conservation genomic research.

Desiccation-induced DNA damage facilitates drug resistance in Mycobacterium tuberculosis

This study shows desiccation-induced DNA damage in Mtb leads to mutations and drug resistance by affecting DNA repair and gene expression.

Curated high-quality genomes of 39 diverse halophilic archaea

The paper presents high-quality chromosome-level genomes of 39 haloarchaeal strains, expanding genomic resources and enabling comparative studies of archaeal biology and virus-host interactions.

Genomic Characterization of the Endangered Medicinal Polypore Agarikon (Laricifomes officinalis syn. Fomitopsis officinalis)

This study presents the first annotated nuclear and mitochondrial genomes of Agarikon, revealing biosynthetic pathways and phylogenetic placement, and provides a foundation for future research on its medicinal properties.

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

The paper presents chromosome-level genome assemblies for four Amaranthus species, revealing conserved sex chromosome inversions and providing resources for evolutionary and agronomic research.

A chromosome-level assembly of an aquatic passerine bird, the northern white-throated dipper, Cinclus cinclus cinclus (Linnaeus, 1758)

The paper presents a chromosome-level genome assembly of the northern white-throated dipper using ONT and Hi-C, resolving previously collapsed dot-chromosomes and showing advantages of ONT over HiFi for repeat-rich regions.

Satellite DNA Editing Enables Meiosis-Independent Chromosome Engineering

This paper demonstrates that CRISPR targeting of satellite DNA allows for meiosis-independent chromosome engineering in aspen, producing stable structural variants in the first generation.

Haplotype-resolved chromosome-level genome assembly of four European white oak species

The paper presents haplotype-resolved chromosome-level genome assemblies for four European white oak species, providing resources for comparative genomics and pangenome studies.

First chromosome scale genome of Acrocomia aculeata

This paper presents the first chromosome-scale genome assembly of Acrocomia aculeata, providing insights for conservation genomics and plant breeding.

Whole genome sequences and annotations of Japanese and French strains of Heterosigma akashiwo

The paper presents high-quality chromosome-scale genome assemblies for two Heterosigma akashiwo strains from Japan and France, revealing extensive synteny and gene content.

Standing genetic variation buffers field populations of Zymoseptoria tritici against seasonal and fungicide selection

The paper analyzes whole-genome sequences from wheat fields to determine how seasonal changes and fungicide use affect genetic variation in Zymoseptoria tritici.

High-quality reference genome of the African hermit spider, Nephilingis cruentata, and sex chromosome evolution in spiders

The paper presents a chromosome-level genome assembly for the African hermit spider and investigates sex chromosome evolution, finding conserved homologous identity but structural divergence.

Caught in transition: facultative intracellularity and genome evolution of Symbiopectobacterium in Rhodnius species

This study examines the distribution, genome evolution, and tissue localization of Symbiopectobacterium in Rhodnius species, revealing its facultative intracellular lifestyle and genome dynamics.

Chromosome-scale genome assembly and annotation of the Vietnamese indica rice cultivar Khang Dan 18

The paper presents a chromosome-scale genome assembly and annotation for the rice cultivar Khang Dan 18, achieving high completeness and quality metrics comparable to other Asian rice genomes.

Valeriana officinalis genome sequence reveals candidate genes for valerenic acid biosynthesis and flavonoid metabolism

This paper reports the first genome sequence of Valeriana officinalis, identifies candidate genes for valerenic acid biosynthesis and flavonoid metabolism, and provides a foundation for studying specialized metabolism in valerian.

A Cesium Chloride Gradient Ultracentrifugation-Based Method for the Isolation of DNA from Diverse Recalcitrant Plant Species for Nanopore Sequencing

This paper introduces a CsCl ultracentrifugation-based DNA isolation method for plant species, improving nanopore sequencing quality and yield compared to traditional CTAB methods.

Near-complete, haplotype-resolved genome assembly of common buckwheat (Fagopyrum esculentum Moench)

The paper presents a near-complete, haplotype-resolved genome assembly of common buckwheat using trio-binning and Hi-C data, providing a valuable resource for genomic research and breeding.

The curious case of a Chilean copepod (Tigriopus aff. angulatus) genome assembly

The paper assembles and annotates a genome for a Chilean Tigriopus copepod population, suggesting it may represent a novel species based on divergence and morphology.