genome assembly

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

This paper presents the first high-quality genome assembly of a cave-dwelling remipede, revealing a repeat-rich genome with extensive gene family turnover and phylogenetic signals.

Population structure of human-infecting and environmental isolates of Coccidioides immitis, the fungus causing Valley fever

The paper analyzes genetic structure and diversity of Coccidioides immitis in environmental and human isolates to understand disease transmission and environmental distribution.

Genome-wide parallelism in divergence and diversity across three Hydrophis sea snake species

This study examines genomic divergence and diversity in three Hydrophis sea snake species, finding shared demographic patterns and linked selection, with chemosensory genes showing elevated diversity.

The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.

Genome assembly of Eucalyptus recurva provides insights into inbreeding and conservation priorities in Australia's rarest Eucalyptus

The paper presents the first T2T genome assembly of Eucalyptus recurva, revealing genomic features and conservation insights.

One species, two lives: cryptic population structure and life-history divergence in a vineyard spittlebug (Aphrophora sp.), a candidate vector for Pierce's disease

The paper analyzes genome data from spittlebugs in vineyards and quasi-natural populations, revealing cryptic population structure, life-history divergence, and insecticide resistance.

Genomic Characterization of the Endangered Medicinal Polypore Agarikon (Laricifomes officinalis syn. Fomitopsis officinalis)

This study presents the first annotated nuclear and mitochondrial genomes of Agarikon, revealing biosynthetic pathways and phylogenetic placement, and provides a foundation for future research on its medicinal properties.

Chromosome-level reference genome assembly of the Saimaa ringed seal (Pusa saimensis) - an ancient glacial relict landlocked pinniped

The paper presents a chromosome-level reference genome for the Saimaa ringed seal, identifies genomic features, and explores evolutionary relationships and adaptations.

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

This study compares TAD conservation and evolution across five cereal species, finding high conservation of TAD boundaries and their role in genome stability during evolution.

A multi-omics view of wax synthesis in the wild cochineal bug, Dactylopius opuntiae

This study provides a genomic, transcriptomic, and proteomic analysis of wax synthesis in Dactylopius opuntiae, identifying 26 FAR genes and their evolutionary expansion.

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

The paper analyzes the genomic diversity of C. tropicalis, finding geographic correlation and hyper-divergent regions linked to environmental adaptation.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Evolutionary dynamics of the Timopheevii wheat lineage

The paper presents genomic resources for the Timopheevii wheat lineage, revealing evolutionary dynamics including homoeologous exchange, genome instability, and geographic range expansion.

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

Genomic diversity of elm trees for future treescapes

The paper analyzes genomic diversity in elm trees to assess the genetic potential of resistant cultivars for restoration.

Geographic structuring of genetic variation differs across two contact zones in the Diglossa carbonaria superspecies

The paper examines genetic differentiation and hybridization in three closely related bird taxa at contact zones using RADSeq data, finding weak genetic differentiation and evidence of introgressive hybridization in one zone.

The first reference genome assembly of the Chilean sea fig (Carpobrotus chilensis)

The paper presents a draft genome assembly of Carpobrotus chilensis, revealing low heterozygosity, high transposable element content, and low sequence divergence from its invasive relative C. edulis.

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Genomic insights into Candidatus Argioplasma dusa, a bacterial symbiont of the wasp spider Argiope bruennichi

The paper reports the genome of Candidatus Argioplasma dusa, a spider symbiont, and finds it has a small genome with limited biosynthetic capabilities, suggesting an endosymbiotic lifestyle.

Whole genome analyses of the endangered Northern abalone (Haliotis kamtschatkana) reveal population differentiation and a genomic signature of a dramatic population decline

The paper uses whole genome resequencing data to analyze population differentiation and decline in Northern abalone, finding genetic structure and a signature of population decline despite previous claims of panmixia.

Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and rare sex

This study examines genome evolution in parthenogenetic nematodes, revealing chromosome fusions, rearrangements, and evidence of rare sexual reproduction events.

Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization

The paper presents haplotype-phased, chromosome-scale genomes of Puccinia hordei isolates, revealing repeat expansion, somatic hybridization, and genome plasticity.

First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America

This paper generates genome-wide data from pre-Ceramic Caribbean individuals, showing genetic continuity with Central America and northern South America and small, locally structured communities.

Eleven deep-sea coral genome assemblies unveil insights into evolution, adaptation, and coral biodiversity

The paper presents 11 deep-sea coral genome assemblies, revealing evolutionary dynamics, environmental adaptation, and genetic differences between deep-sea and shallow-sea corals.

Target capture sequencing provides insights into hybridogenetic water frogs

This study uses target capture sequencing to analyze hybridogenetic water frogs, revealing mtDNA introgression and polyploidy in P. esculentus.

A Seychelles warbler genomic toolkit

The paper develops a genomic toolkit for Seychelles warblers, enabling genetic pedigree assignment and correcting sample identity errors using high-quality genomic data.

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.