genome assembly

This study generates a new genome assembly for Japanese-reared naked mole rats, identifies novel gene models and genomic variations, and provides functional annotations.

The paper presents the first draft genome of the invasive Ludwigia grandiflora subsp. hexapetala, validated through gene expression analysis, and identifies a large number of protein-coding genes.

This paper develops a methylation-conjugation system for Clostridium kluyveri to enable plasmid-based genetic modification and demonstrates its use for expressing a fluorescent reporter.

HiFi-Helper provides a workflow for genome assembly using HiFi reads, achieving quality comparable to older methods with less time and resources.

This paper develops a CPER-based reverse genetics system for rabies virus, enabling the generation of recombinant viruses with various genetic modifications.

This study applies nanopore sequencing to ancient DNA from the Early Jomon period, demonstrating its ability to generate genome-wide data and enable rapid, on-site paleogenomic analysis.

This study identifies three genetic groups in Pacific cod in Japanese waters using SNPs and shows that outlier SNPs improve stock identification accuracy.

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

This paper develops a high-efficiency Rhizobium rhizogenes hairy root transformation system for Vaccinium, achieving up to 80% transformation efficiency and enabling gene validation and genome editing.

This paper introduces SCINKD, a tool to identify sex chromosome linkage groups and curate misassembled regions in a single diploid genome.

The paper sequences the mouse pseudoautosomal region, revealing its structure and evolutionary dynamics.

diempy provides a fast, reference-free method for genome polarisation, enabling analysis of population structure and admixture without pure reference panels.

The paper introduces TTT, an algorithm that resolves assembly graph tangles in genomes, improving the accuracy of complex regions in reference assemblies.

The paper develops a method to resolve collapsed chromosomal segments in polyploid Brachypodium genomes, improving assembly quality and capturing genomic architecture.

This paper presents a high-quality chromosome-level genome assembly of the Kolbroek pig, providing a genetic resource for studying genetic variation and improving breeding programs.

The paper presents a high-quality haplotype-resolved genome assembly of Zoysia japonica and identifies gene expression and regulatory variation between haplotypes.

This paper presents a chromosome-level genome assembly of Acrobeloides nanus, revealing genomic features and adaptations related to parthenogenesis and desiccation resistance.

The paper analyzes non-B DNA motifs in haplotype-resolved human genomes, revealing population-level variation and structural stability patterns in repetitive genomic regions.

This study reports the first complete chloroplast genome of Garcinia binucao, providing genomic resources for conservation and genetic research.

This paper presents the first telomere-to-telomere genome assembly of Dendrobium officinale, identifies tetra-allelic genes, and explores SWEET gene family evolution and mycorrhizal functions.

nanoMDBG improves metagenome assembly from ONT reads, producing more high-quality MAGs with less computational resources than existing assemblers.

The paper presents a chromosome-level genome assembly for the Western Spadefoot, Spea hammondii, using long-read and proximity ligation data, enabling population genomic studies for conservation.

This study uses long-read metagenomic sequencing to analyze Peltigerales lichen symbionts, revealing high transposable element content and their potential role in lichenization evolution.

The paper presents a chromosome-scale genome assembly for Clark's Nutcracker and reports on population genetic findings.

The paper identifies a new genotypic configuration in twins with neurodevelopmental disorder, suggesting a previously unrecognized mutagenesis pathway.

The paper presents a haplotype-resolved genome sequence of a male stinging nettle, confirming structural variation and features associated with sex determination.

FAMeDB is a curated database of fungal proteins involved in aromatic compound metabolism, providing tools for omics analysis and genomic comparisons across 65 fungal species.

This study uses genomic data to analyze evolutionary dynamics of Anopheles gambiae under different insecticidal tools, revealing distinct resistance mechanisms and allele frequency shifts.