genome assembly

Endogenous neuronal DNA double-strand breaks are not sufficient to drive brain aging and neurodegeneration

This study shows that neuronal DNA double-strand breaks, even when accumulated due to loss of C-NHEJ, do not drive brain aging or neurodegeneration in mice.

Designing minimal E. coli genomes using variational autoencoders

This study uses variational autoencoders to generate minimal E. coli genomes, finding 6 out of 100 sampled genomes were viable in a computational model.

MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge

MHConstructor provides a haplotype-informed, high-throughput pipeline for de novo MHC assembly from short read data, improving upon reference-based methods.

CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

This paper compares CRISPR-Cas9 and Cas12a systems for genome editing and large fragment deletions in Aspergillus niger, showing Cas12a's higher efficiency with single gRNA and both systems achieving 100% efficiency with two gRNAs.

Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds

This study assesses the impact of a conservation program on genetic diversity and inbreeding in two French chicken breeds using whole-genome sequencing data.

The first near-complete genome assembly of pig: enabling more accurate genetic research

This paper presents a near-complete pig genome assembly, improving upon the existing reference by closing gaps and enhancing gene prediction, which supports better genetic research and applications.

Haplotype-resolve genome assembly and resequencing provide insights into the origin and domestication of modern rose

This study presents a haplotype-resolved genome assembly and variation map of Rosa hybrida, revealing domestication history and genetic contributions from wild species.

Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

Deciphering of Gorilla gorilla gorilla Immunoglobulin Loci in Multiple Genome Assemblies and Enrichment of IMGT Resources

This study analyzes immunoglobulin loci in four Gorilla gorilla gorilla genome assemblies, revealing variability, copy number variations, and insights into primate immunogenetics.

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae

The paper presents a chromosome-scale genome assembly of D. radicosa and demonstrates its utility for studying Digitaria evolution and Poaceae genetics.

assessPool: a fexible pipeline for population genomic analyses of pooled sequencing data

assessPool provides a pipeline for analyzing pooled sequencing data to infer population structure using FST values and other genomic statistics.

HyLight: Strain aware assembly of low coverage metagenomes

HyLight improves strain-aware metagenome assembly by combining TGS and NGS data, achieving higher accuracy and lower costs than existing methods.

Rapid and cost-effective production of high-quality insect genome sequences

This paper presents a cost-effective method for generating high-quality insect genomes and compares it to existing reference assemblies.

Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it.

This paper evaluates DNA read types for measuring genome contents and sizes, finding mixed results with long reads showing discrepancies between cytometric and assembly measurements.

53BP1 deficiency leads to hyperrecombination using break-induced replication (BIR)

This study shows that 53BP1 deficiency increases BIR-mediated hyperrecombination, leading to genome instability and potential cancer treatment opportunities.

Chromosome-scale genome assembly of acerola (Malpighia emarginata DC.)

This study presents a chromosome-scale genome assembly of acerola using long-read sequencing and genetic mapping, revealing three genetic groups in 60 breeding materials.

Comparative analysis of amphibian genomes: an emerging resource for basic and applied research

The paper evaluates 51 amphibian genomes to assess their utility for functional genomics, finding variation in quality, high transposable element content, and conserved synteny despite divergence.

De-novo Genome of the Edwardsiid anthozoan Edwardsia elegans

The paper reports the de-novo genome of Edwardsia elegans, highlighting genomic conservation and variation within cnidarians.

MORC-1 is a key component of the C. elegans CSR-1 germline gene licensing mechanism

The paper shows MORC-1 overexpression in csr-1 mutants drives gene downregulation by altering chromatin states, revealing its role in CSR-1-mediated gene licensing.

Utilizing Non-Invasive Prenatal Test Sequencing Data Resource for Human Genetic Investigation

The paper develops methods for analyzing low-depth NIPT sequencing data to accurately estimate allele frequencies and genetic effect sizes, enabling population genetic studies.

The Hypolimnas misippus genome supports a common origin of the W chromosome in Lepidoptera

The paper presents genome assemblies of two Hypolimnas species and analyzes the evolution of W chromosomes in Lepidoptera, suggesting a common origin despite conflicting hypotheses.

Sporadic distribution of a new archaeal genetic code with all TAG codons as pyrrolysine

The paper confirms a new archaeal genetic code (Code 34) where TAG codons encode pyrrolysine, showing sporadic distribution and lateral gene transfer.

Genome assembly and genomic architecture of a prominent cold-resistant rapeseed germplasm

The paper assembles a high-quality genome of a cold-tolerant rapeseed cultivar and identifies genomic features associated with cold resistance.

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens)

The paper presents a high-quality genome assembly and annotation for the Florida Scrub-Jay using long-read sequencing and a linkage map, providing tools for studying evolutionary dynamics in conservation populations.

SpLitteR: Diploid genome assembly using linked TELL-Seq reads and assembly graphs

SpLitteR improves diploid genome assembly using linked TELL-Seq reads and assembly graphs, achieving higher contiguity without additional misassemblies.

Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing

Strainy assembles and phases strain haplotypes from long-read metagenome data, outperforming existing methods in accuracy and completeness.

dScaff - an automatic bioinformatics framework for scaffolding draft de novo assemblies based on reference genome data

dScaff scaffolds de novo genome assemblies using reference data, demonstrating its functionality on a Drosophila suzukii genome assembly.

De novo assembly and annotation of the Empoasca fabae mitochondrial genome

This paper assembles and annotates the mitochondrial genome of Empoasca fabae, revealing its gene composition and phylogenetic placement.

Chromosome-level Genome Assembly and Annotation of Petunia hybrida

This paper presents a chromosome-level genome assembly for Petunia hybrida using hybrid sequencing technologies, revealing syntenic relationships and providing a resource for functional genomics.

Nuclear dualism without extensive DNA elimination in the ciliate Loxodes magnus

This study investigates genome development in Loxodes magnus, finding no canonical IESs or editing hallmarks during MIC-to-MAC development, suggesting a loss or streamlining of genome editing processes.