genome assembly

Complete genome sequence and metabolic features of Vreelandella zhaodongensis BS253: A new isolate from hypersaline lakes from Brazilian Pantanal

This paper reports the complete genome sequence and metabolic features of a new extremophile isolate, Vreelandella zhaodongensis BS253, from a hypersaline lake, highlighting its potential for biotechnological applications in carbon capture and sustainable processes.

Asymmetric migration shapes genetic structure of the invasive avian vampire fly (Philornis downsi) across the Galapagos Islands.

This study investigates the genetic structure and dispersal patterns of Philornis downsi across Galapagos Islands using whole genome sequencing, finding asymmetric gene flow and genetic divergence linked to trade winds and shipping routes.

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

A chromosome-level genome assembly of the classical model nematode Panagrellus redivivus for comparative studies of parasitism evolution

The paper presents a chromosome-level genome assembly of Panagrellus redivivus, enabling comparative studies of parasitism evolution by providing a non-parasitic reference genome.

Reaction Norm Modeling of High-Dimensional Genomic and Environmental Data Improves Prediction Accuracy in Winter Wheat

This paper improves genomic prediction accuracy in winter wheat by integrating genotype-by-environment interactions and environmental covariates across multiple environments.

Genome and methylome of the root crop table beet (Beta vulgaris)

The paper presents a chromosome-scale genome and methylome assembly for table beet, identifies candidate genes for geosmin production, and compares it with sugar beet.

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

This study uses PacBio HiFi sequencing to assemble complete Plasmodium falciparum genomes from natural infections, revealing full repertoires of immune-related genes.

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

The paper presents a chromosome-level, haplotype-resolved genome assembly for the European moose, achieving high completeness and gene annotation.

PoLoCo: A reproducible pooled low-coverage workflow for draft genome assembly and allele frequency analysis from ethanol-preserved small non-model invertebrates

Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798)

The paper presents a chromosome-level genome assembly for the Eurasian great grey owl, improving resolution of sex chromosomes and microchromosomes compared to previous assemblies.

High Quality, Long-Read Genome Assemblies of Two Virulent Field Isolates of Pyricularia oryzae from Portugal

Two Portuguese rice-blast fungus isolates were assembled from PacBio HiFi reads into near-complete genomes; one isolate lacks Avr-Pii, Avr-Pia and Avr-Pik yet remains virulent on two rice cultivars.

Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus)

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

A Highly Contiguous Reference Genome for Scalesia gordilloi (Asteraceae), a Critically Endangered Plant Endemic to the Galapagos Islands

This paper presents the first high-quality reference genome for Scalesia gordilloi, a critically endangered plant, using Oxford Nanopore sequencing to enable conservation and comparative genomics studies.

PhAGE Enables One-Step Genome Integration of Large DNA Fragments in Escherichia coli

PhAGE enables one-step integration of ~20 kb DNA fragments into E. coli genome, resolving the trade-off between simplicity and insert size in genome engineering.

The Value of Multi-Year Sampling for Detecting Fine-Scale Population Genetic Structure in Marine Fishes: A Case Study of Juvenile Southern Flounder

The paper uses ddRADSeq to analyze genetic structure in southern flounder over multiple years, finding significant differentiation between regions and temporal variability within estuaries.

The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle

The paper generates chromosome-level assemblies of the mountain pine beetle to study neo-sex chromosome evolution, revealing rapid degeneration and structural divergence in neo-Y chromosomes.

Draft genome assembly of the green-bronze dung beetle, Onthophagus orpheus

The paper presents a high-quality genome assembly for the green-bronze dung beetle, Onthophagus orpheus, and annotates its genes for future ecological and genetic studies.

Engineered orthogonal translation systems from metagenomic libraries expand the genetic code

The paper discovers and engineers an orthogonal translation system using metagenomic data to expand the genetic code with non-canonical amino acids.

Chromosome-level genome assembly of Helichrysum odoratissimum, a medicinal plant from Southern Africa

This paper presents a chromosome-level genome assembly for Helichrysum odoratissimum to support genetic and functional studies.

'PePApipe': a complete bioinformatics analysis pipeline for African Swine Fever Virus genome

PePApipe is a bioinformatics pipeline for ASFV genome analysis that integrates multiple tools into an automated workflow, enabling rapid and reproducible genomic analysis with minimal bioinformatics expertise.

PAT: An Image Analysis Tool for Automated Scoring of Pollen in Alexander-Stained Anthers

The paper introduces PAT, an AI tool for automated pollen viability analysis, and uses it to identify a genetic suppressor of meiotic defects in Arabidopsis.

An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis

The paper develops a low-cost genotyping panel for Yesso scallops to support breeding and disease resistance studies.

Genomic consequences of admixture in an experimentally founded sand lizard population

The paper examines the genomic effects of genetic rescue in a sand lizard population, finding increased diversity and reduced genetic load after admixture.

Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

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.

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.

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.

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.