genome assembly

Trait genetic architecture and population structure determine model selection for genomic prediction in natural Arabidopsis Thaliana populations

The paper evaluates genomic prediction models for 36 traits in Arabidopsis thaliana, finding regression models generally most accurate, with random forest better for biochemical traits.

Inversions Dominate Evolution in the Highly Admixed European Sardine (Sardina pilchardus)

The paper investigates the role of inversions in shaping genetic diversity and population structure in European sardines, finding they drive adaptive allele frequency differences across populations.

Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo

The paper introduces EcoPhylo, a computational workflow to assess genome recovery rates in microbial communities using ribosomal protein phylogeography, applied to human gut and oral cavity data.

Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host

The paper develops a method to identify and sequence multiple RNA virus isolates co-infecting a single host plant, demonstrating its effectiveness on rice yellow mottle virus in Burkina Faso.

Haplotype-resolved genome assembly of the tetraploid potato cultivar Desiree

This paper presents a haplotype-resolved genome assembly for the tetraploid potato cultivar Desiree, along with annotations and epigenetic data, providing a resource for potato research.

ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea

The paper presents a chromosome-level reference genome for Phyllidia flava, a Mediterranean nudibranch, to aid conservation and phylogenetic studies.

Leveraging ancestral recombination graphs for quantitative genetic analysis of rice yield in indica and japonica subspecies

This study uses ancestral recombination graphs to improve quantitative genetic analysis of rice yield in indica and japonica subspecies, showing better predictive ability when combining both subspecies.

Ceratopteris richardii U6 promoters and plants expressing Cas9 endonuclease as tools for efficient genome editing in a fern

The paper identifies U6 promoters and develops Cas9-expressing plants in Ceratopteris richardii to improve genome editing in ferns.

A major update of the genome assembly of Eri silkmoth, Samia ricini.

The paper updates the genome assembly of Samia ricini using long-read technologies and provides functional annotations including gene prediction and piRNA clusters.

North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period

This study uses genomic data from 91 individuals in Ukraine to analyze migration patterns from the Bronze Age to the early modern period, revealing complex ancestry changes and continuity.

ERGA-BGE genome of Erebia palarica Chapman, 1905: a montane butterfly endemic to North-West Iberia

The paper presents the reference genome of Erebia palarica, enabling studies on speciation, hybridization, and population genetics.

ERGA-BGE genome of the Spanish Moon Moth Graellsia isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive

The paper presents the reference genome of the Spanish Moon Moth Graellsia isabellae, which helps resolve its scientific name and supports genetic monitoring of the species.

Genomic prediction of individual inbreeding levels for the management of genetic diversity in populations with small effective size

The paper evaluates methods for predicting inbreeding levels using genomic data in small populations, finding that model-based and rule-based approaches perform well under various conditions.

Genome structural variation in natural Caenorhabditis elegans populations

This study identifies structural variants in wild Caenorhabditis elegans populations using long-read sequencing, revealing their role in phenotypic diversity and adaptation.

Draft genome analysis of Delftia tsuruhatensis IICT-RSP4, a strain with uricase potential isolated from soil

The paper reports the draft genome sequence of Delftia tsuruhatensis IICT-RSP4, an uricase-producing soil bacterium, revealing its potential for antimicrobial, anticancer, and antimalarial secondary metabolites.

A high-quality phased genome assembly of stinging nettle, Urtica dioica ssp. dioica

The paper presents a high-quality phased genome assembly of Urtica dioica using multiple sequencing technologies and a novel Hi-C protocol, revealing structural variation and gene content.

LMNA R644C associates with hepatic steatosis in a large cohort and increases cellular lipid droplet accumulation in vitro

De novo genome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

The paper presents the first reference genome for the red-fronted brown lemur using portable nanopore sequencing conducted in Madagascar, highlighting its potential for conservation genomics and equitable research practices.

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

The paper constructs a near-complete genome assembly for the bearded dragon Pogona vitticeps and characterizes the Z sex chromosome, identifying key genes involved in sex determination.

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

The paper presents a high-quality, telomere-to-telomere genome assembly and annotation for the central bearded dragon, providing insights into its sex determination mechanisms.

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

The paper presents haplotype-resolved genomes for five sea turtle species, revealing conserved synteny and divergence hotspots linked to immune and sensory genes, and population expansion during the Pleistocene.

Shared selection and genetic architecture drive strikingly repeatable evolution in long-term experimental hybrid populations

The study shows that shared selection and genetic architecture lead to repeatable evolution in hybrid sunflower populations over 14 years.

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)

This study presents a chromosome-level reference genome for the Arabian horned viper, revealing insights into venom gene evolution and population history.

xRead: a coverage-guided approach for scalable construction of read overlapping graph

xRead improves scalability and efficiency for constructing read overlapping graphs in long-read sequencing by using a coverage-guided model and heuristic alignment skeleton approach.

Pre-Assembly NGS Correction of ONT Reads Achieves HiFi-Level Assembly Quality

The paper shows that ONT reads corrected by NGS can achieve assembly quality comparable to HiFi-based methods, offering a cost-effective alternative for genome assembly.

Chromosome-scale assembly and annotation of the wildwheat relative Aegilops comosa

The paper presents a chromosome-level genome assembly of Aegilops comosa using PacBio and Hi-C data, annotates 39,063 genes, and identifies a terminal intrachromosomal translocation in chromosome 2M.

Genomic and metabolic characterization of Trueperella pyogenes isolated from domestic and wild animals

This study characterizes the genomic and metabolic features of Trueperella pyogenes from various animal hosts, identifying its non-host-specific nature and antimicrobial resistance genes.

Fast and exact gap-affine partial order alignment with POASTA

POASTA is an optimal algorithm for partial order alignment that improves speed and memory efficiency, enabling larger alignments in bacterial gene datasets.

An exploration of unusual antimicrobial resistance phenotypes in Salmonella Typhi from Blantyre, Malawi reveals the ongoing role of IncHI1 plasmids

Regular Plasmodium falciparum importation onto Bioko Island, Equatorial Guinea, hampers malaria elimination from the island

This study uses genomic data to show that imported Plasmodium falciparum infections from Gabon are contributing to malaria transmission on Bioko Island, highlighting the need for regional control efforts.