genome assembly

Deep Learning for genomic prediction accounting for heterosis in crossbreeding systems

This paper evaluates deep learning's ability to predict genetic values in crossbred populations by capturing heterosis, finding it improves performance when heterosis is present.

A rapid and efficient red-light-activated Cre recombinase system for genome engineering in mammalian cells and transgenic mice

This paper introduces REDMAPCre, a red-light-activated Cre recombinase system that enables rapid and efficient DNA recombination in mammalian cells and mice.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

T2T Gap-free Genome Assembly of Gp03, a Soybean Cultivar with High Genetic Transformation Efficiency

The paper presents a complete T2T genome assembly of the soybean cultivar Gp03, which has high genetic transformation efficiency, providing a valuable resource for soybean breeding.

A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections

The paper presents a chromosome-level genome assembly of the Hispid cotton rat, annotating 24,878 protein-coding genes and identifying genetic innovations.

WISER: spectral whitening of fixed effects for improved breeding value estimation in structured, unbalanced, and genotype-environment-confounded populations

WISER improves breeding value estimation by addressing population structure and genotype-environment confounding through spectral whitening, outperforming LS-means and BLUP across multiple species and traits.

Population Genomics Informs Conservation Strategies for Critically Endangered Kokia Species in Hawaii

This study uses population genomics to assess genetic diversity and structure in three critically endangered Kokia species in Hawaii, informing conservation strategies.

Highly replicated experiments studying complex genotypes using nested DNA barcodes.

The paper introduces a barcode-based method to track combinatorial genotypes in pooled experiments, enabling high-throughput genetic screening and analysis of complex genotype-phenotype relationships.

An enhanced Eco1 retron editor enables precision genome engineering in human cells without double-strand breaks

This paper enhances the Eco1 retron editor for precise genome editing in human cells by improving ncRNA stability and reducing sgRNA extension, achieving editing without double-strand breaks.

A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population

The paper presents a high-quality, gapless diploid reference genome for an Indian population, revealing extensive structural variation and improved performance for genomic analysis in South Asian samples.

From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives

The paper develops de novo chromosome-scale genomes for two Aedes mosquito species and compares them to a reference genome to reveal chromosomal rearrangements and gene expansion differences.

Geographic Genetic Variation in the Introduced Insect Hyphantria cunea Drury in Japan Revealed by RAPD Analysis

The paper uses RAPD analysis to study genetic variation in the invasive fall webworm Hyphantria cunea in Japan, finding two major genetic clusters corresponding to coastal regions.

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Comparing nine Solanaceae genomes reveals a conserved withanolide gene cluster; three of its P450s, expressed in yeast and N. benthamiana, oxidise 24-methyldesmosterol toward the withanoside V aglycone.

Genomic Insights into the Diversity, Antimicrobial Resistance, and Zoonotic Potential of Campylobacter fetus Across Diverse Hosts and Geographies

This study analyzes 114 C. fetus genomes to explore genetic diversity, antimicrobial resistance, and zoonotic potential across hosts and geographies.

High-quality genome assembly of the endemic threatened White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.

The paper presents the first high-quality genome assembly for the White-bellied Sholakili, using Nanopore and Illumina data, and reports its completeness and functional annotations.

Genome report: Genome sequence of the hibiscus mealybug, Nipaecoccus viridis (Newstead), an invasive pest of citrus

The paper presents the de novo genome assembly of the hibiscus mealybug, Nipaecoccus viridis, and reports gene count and repetitive element composition.

Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite

The paper builds a reference genome for Cylicocyclus nassatus, estimates its genetic diversity across regions, and identifies genetic candidates for pyrantel resistance.

The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

This paper assembles the first complete genome of the Northern Dusky Salamander, revealing its miniaturized genome and TE composition.

IMGT(R) Analysis of the Human IGH Locus: Unveiling Novel Polymorphisms and Copy Number Variations in Genome Assemblies from Diverse Ancestral Backgrounds

The paper analyzes the human IGH locus across 15 genome assemblies to identify novel alleles, copy number variations, and polymorphisms, enhancing the IMGT(R) reference directory.

Highly efficient genome editing in Bacillus subtilis via miniature DNA nucleases IscB.

This study develops efficient genome editing tools in Bacillus subtilis using IscB and enIscB, achieving high deletion and integration efficiencies.

A simplified two-plasmid system for orthogonal control of gene expression using light-activated CRISPR effector for mammalian cells

This paper simplifies the LACE optogenetic system from four to two plasmids, showing similar performance with reduced variability.

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

PacBio genome assembly of Olea europaea L. subsp. europaea cultivars 'Frantoio' and 'Leccino' reveal main structural differences in key genes related to salt stress

The paper presents high-quality genome assemblies for two olive cultivars using PacBio HiFi sequencing, revealing structural differences in genes related to salt stress.

Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses

This study shows that low-coverage whole-genome sequencing (lcWGS) accurately reconstructs haplotypes in complex mouse crosses, outperforming SNP arrays and ddRADseq at low sequencing depths.

High-Quality PacBio Genome Assembly of Populus alba L. Villafranca

This study presents a high-quality genome assembly of Populus alba L. Villafranca using PacBio HiFi sequencing, revealing structural variants and genomic features.

Assessment of Ex Situ Conservation Strategies for the Preservation of Domestic South American Camels in Southern Peru: Insights from Mitochondrial DNA Analysis

This study assesses genetic diversity and conservation strategies for alpacas and llamas in Southern Peru using mitochondrial DNA analysis and evaluates the effectiveness of an ex situ germplasm bank.

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

This study uses 30 new palaeogenomes to show that Neolithic expansion into Western Anatolia involved both indigenous assimilation and eastern population influx, with cultural diversity decoupled from genetic differences.

Assessment of the Genetic Diversity of Atlantic Bottlenose Dolphin (Tursiops truncatus) Strandings in the Mississippi Sound (USA)

This study assesses genetic diversity and population structure of Atlantic bottlenose dolphins in Mississippi Sound using whole mitogenomes from stranded animals, identifying four distinct populations.

Chromosome-level genome assembly of the spider mite Tetranychus cinnabarinus

This study presents a chromosome-level genome assembly of the spider mite Tetranychus cinnabarinus, identifying key detoxification genes relevant to pesticide resistance.

Rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice revealed through deep population-level sequencing

This study tracks rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice over 28 days, identifying polymorphisms, phase-variable loci, and spatial variation in the gut.