genome assembly

Single-cell sequencing reveals genome streamlining and functional diversity in ecologically dominant marine protists

The paper generates single-cell genomes from marine protists to reveal genome streamlining and functional diversity in ecologically dominant species.

Is a dam-altered river in the U.S. Southwest a barrier to dispersal for populations of a common lizard, Uta stansburiana?

The study examines whether dams in the U.S. Southwest act as barriers to dispersal for Uta stansburiana lizards, finding low genetic exchange despite varying water conditions.

Chromosome-level genome assembly of the sponge Halisarca dujardinii

This paper presents the first chromosome-level genome assembly of the sponge Halisarca dujardinii, along with mitochondrial genome and comprehensive annotation.

Genomic Analysis Reveals Recent Population Decline and Exceptionally Low Genome-Wide Heterozygosity of the Critically Endangered Philippine Eagle, Pithecophaga jefferyi (Aves: Accipitridae)

The paper analyzes the genomes of 35 Philippine Eagles to reveal recent population decline and exceptionally low genome-wide heterozygosity, highlighting genetic risks for conservation.

GANGE: Achieving Sequencing Without Sequencing With Diffusion Guided Generative Genomic Transformer

GANGE is a deep-learning system that generates accurate genomic sequences from low-coverage, error-prone reads, reducing sequencing costs and enabling regulomics research without genome data.

The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

The paper reports the genome of Paramecium aurelia, revealing tiny germline chromosomes with an exceptionally high recombination rate and a new class of Helitrons at their ends.

Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes

The paper presents the first genome assembly of Abrothrix olivacea and uses it to study gene expression and genetic divergence in kidney tissue across contrasting environments.

A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti

This paper presents a targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti, showing it can replicate WGS population structure analyses and accurately measure genetic admixture.

"Cold" Orthogonal Translation: A Psychrophilic Pyrrolysyl-tRNA Synthetase Boosts Genetic Code Expansion in E. coli

The paper develops a psychrophilic orthogonal translation system for expanding the genetic code in E. coli, showing improved efficiency and versatility compared to mesophilic and thermophilic systems.

Non-uniform chromosomal SNP density biases sites of meiotic crossovers in Drosophila melanogaster

The paper identifies how uneven SNP distribution on the X-chromosome of Drosophila affects meiotic crossover sites, reducing mapping resolution for genetic traits.

A Reference Genome for the Critically Endangered Philippine Eagle (Pithecophaga jefferyi), the National Bird of the Philippines

The paper presents a high-quality reference genome for the critically endangered Philippine Eagle, revealing its evolutionary relationships and population history.

PHYCUT: Scalable multiplex CRISPR/Cas9 editing forgenome engineering in the diatom Phaeodactylumtricornutum

The paper develops PHYCUT, a CRISPR/Cas9 system for multiplex genome editing in the diatom Phaeodactylum tricornutum, demonstrating its use to reduce fucosylation of secreted proteins.

A coordinated regeneration-selection strategy enables genetic transformation and rapid flowering in apple x pear intergeneric hybrids

This study develops a regeneration-selection strategy for apple x pear hybrids to enable genetic transformation and rapid flowering through over-expression of MdFT1.

Living by the sea: chromosome-scale genome assembly and salt gland transcriptomes provide insights into ion regulatory mechanisms in the saline-tolerant mosquito Aedes togoi

This study presents a chromosome-scale genome assembly and transcriptomes of Aedes togoi, revealing ion regulatory mechanisms enabling its saline tolerance.

Genomic landscape of the medieval Hungarian elite from the Szekesfehervar royal necropolis

The paper analyzes shotgun genomes from the medieval Hungarian elite, revealing homogenization through admixture and identifying a previously unrecognized Conquest-period stratum.

Contrasting patterns of seascape genetics in Acropora cf. tenuis and their symbiotic algae.

The paper examines genetic variation in Acropora cf. tenuis corals and their algal symbionts across a reefscape, finding contrasting dispersal patterns between hosts and symbionts.

Synolog: A Scalable Synteny-Based Framework for Genome Architecture Characterization

Synolog identifies orthologs, synteny clusters, and genomic features across species, demonstrating its utility in studying genome evolution and structure.

Telomere-to-telomere genome assembly of Microsporidia sp. MB, a microsporidian symbiont of Anopheles coluzzii isolated from Burkina Faso

The paper presents the first complete telomere-to-telomere genome assembly of Microsporidia sp. MB, revealing genomic features and gene loss associated with its symbiotic lifestyle.

Cryptic diversity and impacts of domestication in the Black Soldier Fly (Hermetia illucens)

The paper analyzes whole genome sequences of Black Soldier Fly populations to reveal cryptic genetic diversity and the impacts of domestication on genetic variation.

Haplotype-resolved Genome Assemblies Reveal Subgenome Origins, Genome Bias and Reticulate Evolution in Wheatgrass Species

This paper presents haplotype-resolved genome assemblies for hybrid wheatgrass and its progenitor, revealing subgenome origins, expression bias, and reticulate evolution.

Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations

This study sequenced ancient and modern genomes from the Ryukyu Archipelago to show genetic differentiation between Ryukyu Jomon and Hondo populations, with admixture occurring around 1,000 YBP.

A High-Quality Genome Assembly of Chaetoceros muelleri Reveals Extensive Gene Duplication, Functional Diversification, and Unique Lineage-Specific Innovation

This study presents a high-quality genome assembly of Chaetoceros muelleri, revealing gene duplication, functional diversification, and TE-mediated genome plasticity.

Ensemble-based genomic prediction for maize flowering-time improves prediction accuracy and reveals novel insights into trait genetic variation

This paper improves genomic prediction accuracy for maize flowering-time traits using an ensemble approach, revealing novel insights into trait genetic variation.

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

The paper catalogs structural and sequence variation in the pennycress pangenome, revealing contrasting evolutionary modes across genomic regions and highlighting the utility of pangenomic resources for crop development.

Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution

The paper identifies immune-deficient bacteria as facilitators of genetic exchange and microbial evolution by enabling horizontal gene transfer of beneficial traits.

Urbanization drives genetic erosion and population structure in a historically connected carnivore population

This study shows urbanization reduces genetic diversity and increases population structure in caracals, with historical connectivity contrasted by recent genetic structuring.

One Sea, Different Whales: Genomics Sheds Light on a Small Population of Fin Whales

The paper sequenced Mediterranean fin whale genomes to assess genetic structure and conservation status, finding moderate diversity but low connectivity with North Atlantic populations.

Haplotype-resolved genome assemblies for Norwegian Red cattle

The paper develops haplotype-resolved genome assemblies for Norwegian Red cattle to improve variant detection and genomic predictions.

Genome assembly of Firmina major, an endangered savanna tree species endemic to China

The paper presents the first high-quality genome assembly of Firmina major, an endangered tree species, providing insights for conservation efforts.

SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.