genome assembly

Chromosome-level reference genome assembly of the Saimaa ringed seal (Pusa saimensis) - an ancient glacial relict landlocked pinniped

The paper presents a chromosome-level reference genome for the Saimaa ringed seal, identifies genomic features, and explores evolutionary relationships and adaptations.

Comprehensive analysis of mulberry genetic diversity based on 1-DNJ content and SNP markers

This study develops SNP markers for mulberry germplasm and analyzes genetic diversity and 1-DNJ content variation, identifying candidate markers for genetic analysis.

Repurposing native non-homologous end joining for multicopy random integration in Wickerhamomyces ciferrii

This paper repurposes the native non-homologous end joining (NHEJ) bias in Wickerhamomyces ciferrii to create a multicopy genome integration platform for metabolic engineering.

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

This study compares TAD conservation and evolution across five cereal species, finding high conservation of TAD boundaries and their role in genome stability during evolution.

A multi-omics view of wax synthesis in the wild cochineal bug, Dactylopius opuntiae

This study provides a genomic, transcriptomic, and proteomic analysis of wax synthesis in Dactylopius opuntiae, identifying 26 FAR genes and their evolutionary expansion.

Chromosome-level genome assembly of the European leaf-toed gecko, Euleptes europaea

The paper presents a chromosome-level genome assembly for the European leaf-toed gecko, providing a high-quality reference for studying genome evolution and sex chromosome dynamics.

Chromosome-level Genome Assembly of the Potato Leafhopper Empoasca fabae (Hemiptera: Cicadellidae)

This paper presents the first chromosome-level genome assembly of the potato leafhopper, revealing synteny with related species and providing a resource for genomic studies.

A meta-analysis of ancient and present-day Central Eurasian genome data to revise archaic hominin ancestry

This study analyzes ancient and present-day Central Eurasian genomes to assess archaic hominin introgression, finding stable levels of Neanderthal and Denisovan ancestry over time.

A chromosome-level genome assembly of a "living fossil", the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

This paper presents the first chromosome-level genome assembly of Lepidurus arcticus, revealing genomic features and comparing it to a related species.

Hidden in the genomic bycatch: insights into genome reorganization and population structure of the parasitic nematode Contortylenchus reversus

The paper presents a chromosome-scale genome assembly of Contortylenchus reversus and analyzes its population structure and host associations using genomic data from host beetles.

Genome sequence of Bacillus paranthracis strain SCM10-01, isolated from the intestinal mucosa of a wild Synallaxis cabanisi collected in Peru.

The paper reports the genome sequence of Bacillus paranthracis SCM10-01 isolated from a wild bird, identifying specific toxin genes but not anthrax-associated genes.

Range wide analysis of genetic diversity and structure gives insights into Rosa gallica L. evolutionary history

This study analyzes the genetic diversity and structure of Rosa gallica across its range to understand evolutionary history and the roles of natural and human factors in its distribution.

Structured Multimodal Deep Learning improves Genomic Prediction in Future Environments

The paper introduces SINN, a structured multimodal deep learning model that improves genomic prediction in new environments by combining statistical decomposition with deep learning, achieving higher accuracy than existing methods.

Chromosome assembly for the Black bean aphid Aphis fabae

The paper presents two chromosome-scale assemblies of the Black bean aphid Aphis fabae using HiFi and Hi-C, revealing expanded UDP-glycosyltransferases linked to insecticide tolerance.

Genetic mapping and genomic prediction for agronomic, grain compositional, and sensing-enabled traits in a cowpea MAGIC population along an environmental gradient

This study identifies genomic hotspots and improves genomic prediction for cowpea traits using a MAGIC population across environmental gradients.

A chromosome-level genome assembly of Thecaphora frezzii, cause of peanut smut, reveals the largest genome among the true smut fungi

The paper presents a chromosome-level genome assembly of Thecaphora frezzii, the largest genome among true smut fungi, and compares it with 49 other smut fungi genomes to explore genomic traits and evolutionary adaptations.

BLink-seq delivers population-scale haplotypes without long reads: a scalable framework for non-model genomics

BLink-seq is a scalable Haplotagging method for generating phased haplotypes and detecting structural variants in non-model species using short-read sequencing.

A chromosome-level genome of the franciscana dolphin, Pontoporia blainvillei

The paper presents the first chromosome-level genome assembly of the franciscana dolphin, enabling phylogenetic and conservation studies.

LightAlign: a lightweight pairwise aligner for memory-constrained HiFi read assembly

LightAlign is a lightweight HiFi read aligner that reduces memory usage for genome assembly in resource-constrained settings.

The genome sequence of Seabra's wing-gland bat, Cistugo seabrae Thomas, 1912

The paper presents a high-quality genome assembly for the Seabra's wing-gland bat, Cistugo seabrae.

A Telomere-to-telomere genome of the hibernating fat-tailed dwarf lemur (Cheirogaleus medius)

The paper presents a telomere-to-telomere genome assembly of the fat-tailed dwarf lemur, providing a high-quality genomic resource for studying hibernation and conservation.

FORGEPHAST: A fast, haplotype-first complex population and phenotype simulator for biobank-scale simulation

FORGEPHAST simulates large synthetic cohorts with controlled genetic and phenotypic properties, showing polygenic risk score performance varies by phenotype architecture, ancestry, and variant coverage.

Range-wide genetic population structure and environmental adaptation in the eastern oyster (Crassostrea virginica) provides insight for aquaculture

This study identifies genetic population structure and adaptive loci in eastern oysters across their range, revealing human impacts and providing targets for climate-resilient aquaculture.

Common schizophrenia heritability concentrates in an evolutionarily young, brain-regulatory subset of fine-mapped credible-set variants

The paper identifies a young, brain-regulatory subset of schizophrenia risk variants that concentrate heritability after accounting for age, frequency, and selection signals.

A consensus genome sequence for the social amoeba Dictyostelium giganteum

The paper generates a consensus genome sequence for Dictyostelium giganteum, analyzing its structure, gene content, and evolutionary relationships with other Dictyostelium and Entamoeba species.

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias

The paper presents a high-accuracy T2T rhesus macaque genome assembly, identifies subtelomeric repeats as a challenge, and reveals new genomic features and functional elements in these regions.

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

The paper presents whole genome sequences of two elasmobranchs, analyzing genome size dynamics and genomic architecture, revealing correlations between chromosome size, repetitive elements, and gene duplication patterns.

The complete genome of a songbird

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

A Complete Genome for the Common Marmoset

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.