genome assembly

Genetic structure of mesophotic and shallow Acropora aculeus on isolated atolls of Eastern Australia

This study examines the genetic structure of Acropora aculeus across depths and regions, finding strong geographic differentiation but no depth-related genetic structuring.

Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis

The paper investigates genetic diversity and sex differentiation in Lutzomyia longipalpis, identifying sex chromosomes and population structure across South America.

Cytonuclear analysis of barley spike traits using a cytoplasm-aware population

The paper develops a cytoplasm-aware population to study cytonuclear interactions in barley, identifying cytoplasmic effects on spike traits and improving genomic prediction.

Simple Growth Conditions Improve Targeted Gene Deletion in Cryptococcus neoformans

This study shows that growing Cryptococcus neoformans in unbuffered YNB media improves gene deletion efficiency using short homology arms.

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

This study constructs a haplotype-phased genome assembly for Haliotis gigantea and identifies non-syntenic homologous chromosomes with structural variations that may contribute to functional diversification.

De novo genome assemblies of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea

The paper presents high-quality de novo genome assemblies for two dwarf honey bee species using hybrid sequencing, showing improved contiguity and completeness compared to previous studies.

A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations

The paper presents a new chromosome-level genome assembly for the western painted turtle, improving upon a previous fragmented assembly and revealing novel genes and transcript isoforms.

What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken?

The paper reanalyzes a chicken genome assembly to correct a previously reported complex chromosomal rearrangement at the Fm locus, showing *Fm_2 is correct instead of *Fm_1 due to assembly errors.

Geometric deep learning framework for de novo genome assembly

This paper introduces GNNome, a geometric deep learning framework for de novo genome assembly that improves contiguity compared to existing tools across multiple species.

Improving hifiasm haplotypes for autopolyploid genome assemblies using constraint programming

The paper improves hifiasm haplotype contigs for autopolyploid genomes by adding protein distribution constraints, enhancing balance and BUSCO scores.

A high-quality chromosome-level genome of an undescribed Meretrix species using Nanopore and Hi-C technologies

The paper presents three reference genomes for Meretrix species, including a chromosome-level assembly using Nanopore and Hi-C technologies, and reports genomic insights for conservation.

Chromosome-level genome assembly of Tamarindus indica

This study presents the first chromosome-level genome assembly of Tamarindus indica, revealing a whole-genome duplication event and gene expression divergence.

Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.

The paper presents a telomere-to-telomere assembly of the Trypanosoma cruzi genome, revealing a 32-chromosome karyotype with conserved structures and identifying a tetraploid chromosome 16.

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

This paper presents a telomere-to-telomere rabbit genome assembly using haploid embryonic stem cells, achieving high completeness and enabling new annotations.

Complete genome sequences of Fusobacterium watanabei sp. isolates

The paper reports the complete genome sequences of eight clinical isolates of Fusobacterium watanabei and classifies them within the 'Fusobacterium nucleatum_J' group.

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

De novo genome assembly of an interspecific hybrid grapevine 'Maeve'

This paper reports the de novo genome assembly of the interspecific hybrid grapevine 'Maeve', revealing its origin from hybridization between an unknown V. vinifera cultivar and V. riparia Gloire.

Population and adaptation history of 739 Thlaspi arvense natural accessions

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

THE HAPLOTYPE-RESOLVED AND CHROMOSOME-SCALE GENOME OF VACCINIUM STAMINEUM: A NEW SOURCE OF GENETIC VARIABILITY FOR BLUEBERRY BREEDING

This study presents the first haplotype-phased reference genome of V. stamineum, a blueberry wild relative, revealing genetic traits useful for breeding programs.

Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution

This paper presents two new Kudoa genomes assembled from contaminated fish samples, revealing conserved gene order and rapid sequence evolution despite genomic simplification.

CASCADE-Cas3 Enables Highly Efficient Genome Engineering in Streptomyces Species

The paper introduces a type I-C CRISPR system, pCRISPR-Cas3, for efficient genome engineering in streptomycetes, outperforming Cas9-based systems in deletion and substitution capabilities.

Strategic targeting of Cas9 nickase expands tandem gene arrays

The paper introduces BITREx, a method using Cas9 nickase to expand tandem gene arrays in yeast and mammalian cells.

The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout

This study produces a chromosomal-level genome assembly for westslope cutthroat trout and identifies interspecific chromosomal rearrangements with rainbow trout.

Chromosome-level reference genome assembly for the protected resource plant, Zenia insignis

This study presents the first nuclear genome assembly for Zenia insignis, a threatened plant species in the Fabaceae family, providing a resource for phylogenomic research.

Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer

The paper presents finished genome assemblies of 15 Variovorax isolates, revealing significant diversity in genome architecture and mechanisms of secondary replicon acquisition.

Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.) at the Botanical Garden of the University of Padua (Italy)

This study presents the first chromosome-level genome assembly of the 400-year-old Goethe's Palm, providing insights into its TE landscape and miRNA annotation for conservation genomics.

Genome Report: Improved chromosome-level genome assembly of the American cockroach, Periplaneta americana

The paper presents a high-quality chromosome-level genome assembly of the American cockroach, Periplaneta americana, using PacBio and Hi-C data, improving upon previous incomplete references.

A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies

This paper presents a high-quality chromosome-scale genome assembly for the Australian alpine skink Bassiana duperreyi using long-read technologies, achieving high completeness and providing a resource for sex determination and thermolabile sex reversal studies.

Chromosome-level genome assembly and annotation of the chaetognath Flaccisagitta enflata

The paper presents the first chromosome-level genome assembly of Flaccisagitta enflata, providing a resource for comparative genomic studies in Chaetognatha and Gnathifera.

The 229 chromosomes of the Atlas blue butterfly reveal rules constraining chromosome evolution in Lepidoptera

The study presents a chromosome-level genome assembly of the Atlas blue butterfly, revealing constraints on chromosome evolution in Lepidoptera through extensive fission and fusion events.