genome assembly

Chromosome-level genome assembly of the Endangered scaly-sided merganser Mergus squamatus with insight into its demographic history

The paper presents a chromosome-level genome assembly for the scaly-sided merganser and analyzes its demographic history using genomic data.

Comparative analysis of genomic prediction approaches for multiple time-resolved traits in maize

This study compares genomic prediction methods for multiple time-resolved traits in maize, finding MegaLMM excels in snapshot accuracy while dynamicGP is better for longitudinal accuracy.

Telomere-to-telomere assembly detects genomic diversity in Canadian strains of Borrelia burgdorferi

The paper develops a genome assembly pipeline to analyze Borrelia burgdorferi strains, revealing genomic diversity at telomeres and plasmids across Canadian isolates.

Genetic diversity, population structure and differentiation of farmed and wild African catfish (Clarias gariepinus) in Nigeria

This study examines genetic diversity and population structure of farmed and wild African catfish in Nigeria, finding higher genetic diversity in wild populations and evidence of farmed fish escaping into the wild.

First Whole-Genome Assembly of the Galapagos Petrel (Pterodroma phaeopygia) Using Oxford Nanopore Sequencing to Advance Conservation Genomics in a Critically Endangered Seabird

Complete genome sequence assembly elucidates evolution and regulation of 5S rDNA loci in the greater duckweed Spirodela polyrhiza

The paper resolves the molecular architecture of 5S rDNA loci in Spirodela polyrhiza using long-read sequencing and fluorescence in situ hybridization, revealing structural and regulatory differences between loci.

Chromosome-level genome assembly and annotation of the degu (Octodon degus)

This paper presents a chromosome-level genome assembly and annotation for the degu, improving contiguity, completeness, and gene annotation compared to previous assemblies.

NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data

NanoSimFormer generates high-fidelity nanopore sequencing signals optimized for accurate basecalling, outperforming existing simulators across multiple datasets and tasks.

Directed evolution for cell separation in natural isolates of budding yeast reveals selection to deactivate AMN1 and the Rim101 pathway in haploids and selection in favor of Hawthorne's deletion in diploids

The paper evolves natural yeast isolates to select for cell separation, identifying AMN1 deactivation and Rim101 pathway mutations in haploids, and Hawthorne's deletion in diploids as key adaptations.

Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

This study presents a gap-free, phased genome assembly of tobacco, revealing subgenomic diversification of centromeres after allopolyploidization.

Engineering the C. elegans genome with a nested, self-excising selection cassette

This paper introduces a new genetic tool, NSEC, to improve genome engineering in C. elegans by enabling homozygous lines for essential genes before marker excision.

BMI1-mediated heterochromatinization represses G-quadruplex DNA formation to maintain genomic stability during replication

The paper shows BMI1 represses G-quadruplex DNA formation by heterochromatinization, preventing replication stress and genomic instability in human cells.

Conservation genomics of desert tortoises (Gopherus agassizii) in the Colorado Desert

The paper defines management units (MUs) for desert tortoises using genetic data and a migration threshold, identifying two subpopulations as MUs despite recent immigration.

Revisiting the genetics of Lake Constance Coregonids using lake-wide whole genome sequencing

The paper uses whole genome sequencing to assess stock composition, spatial distribution, and genetic diversity of Lake Constance whitefish, revealing strong admixture and calling for re-evaluation of management practices.

Scaling perturbations: beyond genome-scale CRISPR screens

The paper introduces two technologies to enhance CRISPR screening, enabling large-scale genetic interaction mapping in human cells using non-fitness phenotypes.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Chromosome-scale genomes of Dugesia reveal contrasting modes of genome size evolution and structural stability in flatworms

The paper presents chromosome-scale genomes of four Dugesia species, revealing genome size evolution and structural instability in flatworms through comparisons with Schmidtea mediterranea.

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

The paper presents a chromosome-level genome assembly of Gerbera hybrida using HiFi and Hi-C technologies, providing annotated nuclear, mitochondrial, and chloroplast genomes.

Genetic Structure and Diversity of Amaranth Populations across Multi-Environmental Sites in Burkina Faso Revealed by Simple Sequence Repeats (SSRs) and Genotyping-by-Sequencing (GBS)

The paper uses SSR and GBS to analyze genetic diversity and structure of Amaranthus species in Burkina Faso, revealing two major genetic groups and morphotype-based clustering.

High-quality genome assemblies of diploid Bromus species enhance understanding of genome complexity and uncover large DNA satellite structures.

The paper presents high-quality genome assemblies of two diploid Bromus species, revealing centromeric repeats, sub-telomeric repeats, and transposable elements, and identifies population structure and hybrid genomic contributions.

Retroelement expansions underlie genome evolution in stingless bees

This study compares genome evolution in two stingless bee species, showing retroelement expansions drive heterochromatin differences and chromosomal rearrangements.

High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

The paper presents a high-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii', revealing detailed gene content and structure.

Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution

This study presents chromosome-scale genome assemblies of two dodder species, revealing genomic features linked to parasitism and polyploid evolution.

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

This study presents a chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping, revealing a genome twice the size of Arabidopsis thaliana.

MoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment

MoGAAAP automates genome assembly and annotation using HiFi and other long-read data, producing quality assessments for comparative genomics.

Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta

This paper presents a chromosome-scale genome assembly for Oxalis stricta, revealing its allotetraploid nature and synteny with related species.

DipGNNome: Diploid de novo genome assembly with geometric deep learning and beam-search

DipGNNome introduces a deep learning framework for diploid genome assembly using graph neural networks and beam-search, achieving results comparable to state-of-the-art methods.

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

This study evaluates room temperature preservation methods for mosquitoes to generate high-quality reference genomes, finding that squished samples in ethanol or Allprotect work best for Hi-C data.

The first chromosome-level annotated reference genome for Chrosomus eos, the northern redbelly dace

The paper presents a chromosome-level reference genome for Chrosomus eos and analyzes its syntenic relationship with the zebrafish genome.