genome assembly

Novel linkage disequilibrium-based genotype-by-environmental interaction method for genomic prediction of cotton yield and fibre quality traits

This paper develops a GEI-based genomic prediction method for cotton traits using dimensionality reduction and Bayesian models, showing better performance than deep learning approaches.

Low genetic diversity in Colobus vellerosus populations in Kikele Sacred and Okuta Kobunan Forests, Benin

The study analyzes genetic diversity in two small populations of Colobus vellerosus in Benin using mitochondrial markers, finding very low diversity due to a potential genetic bottleneck.

Enhanced Bacillus subtilis natural competence enables multiplexed genome and spore engineering

This study improves natural transformation in Bacillus subtilis for genome and spore engineering by optimizing induction systems and culture conditions, achieving higher transformation efficiency and multiplex spore display.

Haplotype-resolved genome of autotetraploid alfalfa (Medicago sativa) Regen-SY27x uncovers large scale structural variation and resistance gene dynamics

The paper presents a haplotype-resolved genome assembly of autotetraploid alfalfa, revealing extensive structural variation and resistance gene dynamics.

Genome Dynamics and Chromosome Structural Variations in Histoplasma ohiense, a fungal pathogen of humans

This study presents the first telomere-to-telomere genome assemblies for Histoplasma ohiense and identifies genome plasticity, including translocations and transposon activity, in clinical isolates.

BioBloom, a method for barcoded saturation mutagenesis of an entire bacterial genome

BioBloom enables whole-genome barcoded saturation mutagenesis in E. coli, identifying beneficial mutations under salt and antibiotic selection with high coverage and efficiency.

CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants

CLCNet improves genomic prediction accuracy in plants by integrating contrastive learning and chromosome-aware feature selection, outperforming existing models across four crop species and ten traits.

Efficient genomic prediction at reduced training size and moderate marker density in an expanded aus-NAM population of rice

This study evaluates genomic prediction and GWAS in an expanded rice NAM population, finding that prediction accuracy plateaus at moderate marker density and training size, while GWAS benefits from higher density.

Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation

The paper presents the genome sequence of Digitalis purpurea and identifies genetic variations associated with flower color and morphology.

Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

The paper presents haplotype-phased, near chromosome-scale genome assemblies for two poplar rust fungi species, improving contiguity and enabling analysis of genome architecture and virulence genes.

High-resolution, genotype-free mapping of genetic variation with CRI-SPA-Map

The paper introduces CRI-SPA-Map, a genetic mapping strategy in yeast that identifies causal genetic variants for phenotypic differences without genotyping.

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

This study constructs a watermelon super-pangenome from 138 genomes, identifies over a million structural variants, and develops genomic prediction models for 18 traits to advance precision breeding.

Reference genome assembly of a tetraploid accession of the tuber crop Tropaeolum tuberosum

This paper presents a high-quality reference genome assembly for a tetraploid accession of Tropaeolum tuberosum, enabling genomic studies and applications in breeding and conservation.

Chromosome-level reference genome of the beach false foxglove, Agalinis fasciculata (Orobanchaceae)

The paper presents the first chromosome-level reference genome for Agalinis fasciculata, revealing genomic features and evolutionary insights into parasitism in Orobanchaceae.

A new evolution-based genomic prediction model forecasts yield performance across environments and future climates and identifies adapted maize landraces

The paper introduces a genomic prediction model that forecasts yield performance across environments and future climates and identifies adapted maize landraces by integrating genomic offset and gene diversity.

Chromosome-level genome assembly of macroalgae Gracilariopsis lemaneiformis

This study presents a chromosome-level genome assembly of Gracilariopsis lemaneiformis using long-read and Hi-C data, revealing gene annotations and repeat elements, and constructing a phylogenetic tree to estimate divergence times.

Genetic mapping of Dutch elm disease resistance

The paper constructs a linkage map of the elm genome and identifies genomic regions associated with Dutch elm disease resistance from resistant species.

Target capture sequencing provides insights into hybridogenetic water frogs

This study uses target capture sequencing to analyze hybridogenetic water frogs, revealing mtDNA introgression and polyploidy in P. esculentus.

SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis

This study shows that SIRT7 maintains genome stability in aging mouse testes by regulating H3K36ac, preventing premature loss of spermatogonia and meiotic defects.

A telomere-to-telomere (T2T) pig genome assembly reveals Y chromosome diversity and structural variations of Wuzhishan pigs

This study assembles a high-quality telomere-to-telomere genome of Wuzhishan pigs, revealing genetic diversity and structural variations compared to a previous assembly.

Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae)

The paper presents a chromosome-level genome assembly for the invasive erythrina gall wasp, Quadrastichus erythrinae, and its endosymbiont Wolbachia pipientis, revealing genomic features and evolutionary insights.

A high-quality telomere-to-telomere LSDV genome assembly

The paper presents a high-quality telomere-to-telomere assembly of the LSDV genome using long-read sequencing, resolving structural ambiguities and improving genomic analysis.

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

Focal inbreeding and clonal transmission of Plasmodium vivax in pre-elimination Vietnam

This study analyzes genomic diversity of Plasmodium vivax in Vietnam, finding decreasing infection complexity, increasing clonal inbreeding, and stable drug resistance allele frequencies over a 10-year period.

Genetic parameters and sex-specific architecture of observed and latent fertility phenotypes in a closed breeding nucleus of an Arctic salmonid

The paper estimates genetic parameters and sex-specific architecture of fertility traits in Arctic charr, identifying genetic correlations and trade-offs affecting reproductive success.

Functional characterisation of an essential neo-chromosome III in Sc2.0 strain reveals opportunities and challenges for genome minimisation in Sc3.0

The paper engineers an essential neo-chromosome III in yeast to enable genome minimisation by relocating essential genes, demonstrating stability and cross-species complementation.

MutaPhy: A clade-based framework to detect genotype-phenotype associations on phylogenetic trees

MutaPhy detects genotype-phenotype associations in pathogens by analyzing phylogenetic trees, revealing lineage-level associations while reducing false positives.

A Seychelles warbler genomic toolkit

The paper develops a genomic toolkit for Seychelles warblers, enabling genetic pedigree assignment and correcting sample identity errors using high-quality genomic data.

First insight into genetic diversity of two sympatric marten species between the Alps and Adriatic islands

This study compares genetic diversity and structure between two sympatric marten species in Croatia and Slovenia, finding significant structuring in pine martens and weak structure in stone martens.

Improved genome assembly of double haploid Prunus persica siblings Lovell 2D and Lovell 5D and the peach NLRome

The paper improves the genome assembly of two peach doubled haploid varieties using third-generation sequencing and enhances gene and NLR annotations.