genome assembly

A chromosome-level genome of the king penguin (Aptenodytes patagonicus): a resource for linking genotype to fitness in a long-lived vertebrate

The paper presents a high-quality chromosome-level genome of the king penguin, improving assembly contiguity and annotation for studying genotype-fitness relationships.

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system

This study optimizes a genome editing system for Cupriavidus necator H16, achieving high editing efficiency using an improved SIBR-Cas system.

Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.

The paper analyzes P. knowlesi genomes from Sabah, Malaysia, to identify genetic subpopulations and introgression events linked to environmental factors and host adaptation.

The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family

This paper reports the complete genome of Candidatus Paracoxiella cheracis, revealing insights into its pathogenesis and phylogeny within the Coxiellaceae family.

De novo Genome Assembly and Annotation of Manouria impressa

The paper presents the first de novo genome assembly of Manouria impressa using long-read and Hi-C technologies, providing a resource for evolutionary and conservation studies.

Mechanisms of G-gene heterogeneities and a new method of genotyping of human metapneumovirus

The paper analyzes G-gene heterogeneities in human metapneumovirus (HMPV) and proposes a new genotyping method based on protein length and sequence differences.

Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds

Mapler: Assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads

Mapler evaluates Hi-Fi long read metagenome assemblies, providing metrics to assess quality and identify bottlenecks in genome reconstruction.

Genomes of two indigenous clams Anomalocardia flexuosa (Linnaeus, 1767) and Meretrix petechialis (Lamarck, 1818)

The paper presents chromosomal-level genome assemblies for two clams using PacBio HiFi and Omni-C reads, providing genomic resources for conservation and ecological studies.

GoldPolish-Target: Targeted long-read genome assembly polishing

GoldPolish-Target polishes targeted regions of genome assemblies, reducing errors and improving accuracy with lower computational demands.

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

The paper analyzes the genomes of spider monkeys and northern muriquis to assess genetic diversity, load, and divergence, finding no alignment between genetic diversity and endangerment status, higher genetic load in wild populations, and divergence linked to environmental factors.

Genomic and morphological characterisation of a novel iridovirus, bivalve iridovirus 1 (BiIV1), infecting the common cockle (Cerastoderma edule)

The paper characterizes a novel iridovirus, BiIV1, associated with cockle mortality, finding it prevalent in moribund cockles and sharing genomic features with other invertebrate iridoviruses.

HP1-enhanced chromatin compaction stabilizes a synthetic metabolic circuit in yeast

This paper shows that expressing HP1 homologues in yeast increases chromatin compaction, reducing mutation and recombination rates, and improving the stability of synthetic metabolic circuits.

Integrative Assessment of Pathogenic Bacterial Genomes: Insights from Quality Metrics

This study assesses the quality of 474 pathogenic bacterial genomes using completeness, contiguity, and accuracy metrics, highlighting the importance of integrated quality control in public genomic databases.

Improved Genomic Prediction Performance with Ensembles of Diverse Models

The paper shows that combining multiple genomic prediction models improves accuracy and reduces errors in predicting crop traits, supporting the Diversity Prediction Theorem.

3D Reconstruction Enables High-Throughput Phenotyping and Quantitative Genetic Analysis of Phyllotaxy

This study uses 3D reconstruction from 2D images to measure phyllotaxy in sorghum, showing its feasibility for genetic analysis and breeding.

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Lagenorhynchus cruciger) Genome

This paper presents a high-quality genome assembly of the hourglass dolphin using Oxford Nanopore sequencing, achieving high contiguity and completeness for marine mammal genomics.

Gearing up Golden Braid assembly for plant synthetic genomics with RepTiles

The paper introduces RepTiles, a system for generating random DNA segments for synthetic genomics, enabling the construction of ultra-long synthetic DNA in Physcomitrium patens.

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

The paper investigates genome dynamics in mosses using chromosome-scale assemblies, finding extensive synteny alongside dynamic gene space driven by de novo gene birth and loss.

High-quality genome assembly for the genetically improved Abbassa Nile tilapia enables the reconstruction of X and Y haplotypes

The paper presents a high-quality genome assembly for the GIANT Nile tilapia strain, enabling the reconstruction of X and Y haplotypes and identifying sex determination loci on LG23.

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

The paper assembles and annotates the genomes of two teinturier grapevine varieties, Dakapo and Rubired, providing genetic resources for studying pigmentation and other traits.

The first chromosomal-level genome assembly of an allotetraploid oyster

The paper presents the first chromosomal-level genome assembly of an allotetraploid oyster, providing a genetic resource for studying genome biology and polyploid breeding.

A newly developed whole genome sequencing protocol enables early tracking of Enterovirus D68 molecular evolution.

This paper develops a whole-genome sequencing protocol for EV-D68 that enables early tracking of its molecular evolution using clinical samples.

Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi)

This study presents the first draft genome assembly of the Visayan Spotted Deer using Illumina sequencing, providing genomic resources for conservation and evolutionary research.

Strong sequencing bias in Nanopore and PacBio prevents assembly of Drosophila melanogaster Y-linked genes

The paper identifies sequencing bias in Nanopore and PacBio that prevents assembly of Y-linked genes in Drosophila melanogaster, highlighting issues with read initiation, elongation, and base-calling near satellite sequences.

The Greenland shark genome: insights into deep-sea ecology and lifespan extremes

This paper presents the first chromosome-level genome assembly of the Greenland shark, identifying genetic features associated with its extreme longevity and deep-sea adaptations.

Phenotypic and genetic heterogeneity of Acinetobacter baumannii in the course of a chronic infection

This study examines genetic and phenotypic changes in Acinetobacter baumannii during a five-year UTI without antibiotic treatment, revealing genome reduction and loss of adhesion capacity but conserved colistin resistance.

Pneumo-Typer: integrated genomic surveillance tool for capsule genotype, serotype and sequence type in Streptococcus pneumoniae informs vaccine strategies

Pneumo-Typer identifies capsule genotype variations in Streptococcus pneumoniae genomes, revealing CapT diversity and informing vaccine strategies.

Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231 cell line

The paper examines genomic diversity within the MDA-MB-231 breast cancer cell line across sublines, identifying intraline heterogeneity driven by single nucleotide variants and copy number alterations.

Draft genome of the marine Entamoeba species reveals reduction in the gene family repertoire associated with pathogenicity and lateral gene transfer for adaptation to the marine environment

The paper presents the genome and transcriptome of E. marina, revealing reduced pathogenicity-related genes and evidence of lateral gene transfer for marine adaptation.