Diagenode

Newly added

150 publications found.

SUMO protease FUG1, histone reader AL3 and the PRC1 Complex areintegral to repeat-expansion induced epigenetic silencing in Arabidopsisthaliana
Published: December, 2023

Abstract: Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich’s ataxia in humans1. The molecular mechanisms underlying repeat expansion-...
Read more »

Pre-diagnosis plasma cell-free DNA methylome profiling up to seven years prior to clinical detection reveals early signatures of breast cancer
Published: February, 2023

Abstract: Profiling of cell-free DNA (cfDNA) has been well demonstrated to be a potential non-invasive screening tool for early cancer detection. However, limited studies have investigated the detectability of cfDNA methylation markers that are predictive o...
Read more »

Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients’ plasma
Published: February, 2023

Abstract: During cancer development, host’s tumorigenesis and immune signals are released to and informed by circulating molecules, like cell-free DNA (cfDNA) and RNA (cfRNA) in blood. However, these two kinds of molecules are still not systematically compa...
Read more »

Low affinity CTCF binding drives transcriptional regulation whereas high affinity binding encompasses architectural functions
Published: February, 2023

Abstract: CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS). Using a conditional mous...
Read more »

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen.
Published: February, 2023

Abstract: Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for non-model organisms. Sequencing approaches that rely on HMW DNA have been limited to larger ...
Read more »

Targeting high glucose-induced epigenetic modifications at cardiac level: the role of SGLT2 and SGLT2 inhibitors.
Published: February, 2023

Abstract: BACKGROUND: Sodium-glucose co-transporters (SGLT) inhibitors (SGLT2i) showed many beneficial effects at the cardiovascular level. Several mechanisms of action have been identified. However, no data on their capability to act via epigenetic mechani...
Read more »

Myelodysplastic Syndrome associated TET2 mutations affect NK cell function and genome methylation.
Published: February, 2023

Abstract: Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders, representing high risk of progression to acute myeloid leukaemia, and frequently associated to somatic mutations, notably in the epigenetic regulator TET2. Natural Killer (NK) cel...
Read more »

Species-specific regulation of XIST by the JPX/FTX orthologs.
Published: February, 2023

Abstract: X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolv...
Read more »

Noncanonical regulation of imprinted gene Igf2 by amyloid-beta 1-42 in Alzheimer's disease.
Published: February, 2023

Abstract: Reduced insulin-like growth factor 2 (IGF2) levels in Alzheimer's disease (AD) may be the mechanism relating age-related metabolic disorders to dementia. Since Igf2 is an imprinted gene, we examined age and sex differences in the relationship betw...
Read more »

The genome sequence of the Grey Ermine, Yponomeuta sedella (Treitschke, 1832)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Yponomeuta sedella (the Grey Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 658 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudo...
Read more »

The genome sequence of the Mouse Moth, Amphipyra tragopoginis (Clerck 1759)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Amphipyra tragopoginis (the Mouse Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 806 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudom...
Read more »

The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Acronicta leporina (the Miller; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecul...
Read more »

The genome sequence of a soldier beetle, Podabrus alpinus (Paykull, 1798)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Podabrus alpinus (soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence is 777 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudom...
Read more »

The genome sequence of a beetle-killing wasp, Tiphia femorata (Fabricius, 1775)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Tiphia femorata (a beetle-killing wasp; Arthropoda; Insecta; Hymenoptera; Tiphilidae). The genome sequence is 276 megabases in span. Most of the assembly (98.73\%) is scaffolded into 12 chromo...
Read more »

The genome sequence of the Green-brindled Crescent, Allophyes oxyacanthae (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Allophyes oxyacanthae (the Green-brindled Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 458 megabases in span. The whole assembly is scaffolded into 31 chromosom...
Read more »

The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudom...
Read more »

The genome sequence of a tachinid fly, Thecocarcelia acutangulata (Macquart, 1850)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Thecocarcelia acutangulata (a tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 693 megabases in span. Most of the assembly is scaffolded into six chromosomal pse...
Read more »

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing.
Published: February, 2023

Abstract: Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases . Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prio...
Read more »

Detailed molecular and epigenetic characterization of the Pig IPECJ2 and Chicken SL-29 cell lines
Published: February, 2023

Abstract: The pig IPECJ2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. ...
Read more »

Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis
Published: February, 2023

Abstract: Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4m...
Read more »

Histone remodeling reflects conserved mechanisms of bovine and human preimplantation development.
Published: February, 2023

Abstract: How histone modifications regulate changes in gene expression during preimplantation development in any species remains poorly understood. Using CUT\&Tag to overcome limiting amounts of biological material, we profiled two activating (H3K4me3 and ...
Read more »

Epigenetic regulation of plastin 3 expression by the macrosatellite DXZ4 and the transcriptional regulator CHD4.
Published: February, 2023

Abstract: Dysregulated Plastin 3 (PLS3) levels associate with a wide range of skeletal and neuromuscular disorders and the most common types of solid and hematopoietic cancer. Most importantly, PLS3 overexpression protects against spinal muscular atrophy. D...
Read more »

The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis.
Published: February, 2023

Abstract: BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene tha...
Read more »

A dataset of definitive endoderm and hepatocyte differentiations from human induced pluripotent stem cells.
Published: February, 2023

Abstract: Hepatocytes are a major parenchymal cell type in the liver and play an essential role in liver function. Hepatocyte-like cells can be differentiated in vitro from induced pluripotent stem cells (iPSCs) via definitive endoderm (DE)-like cells and h...
Read more »

Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes.
Published: February, 2023

Abstract: Enhancer activation serves as the main mechanism regulating signal-dependent transcriptional programs, ensuring cellular plasticity, yet central questions persist regarding their mechanism of activation. Here, by successfully mapping topoisomerase...
Read more »

Methylation and expression of glucocorticoid receptor exon-1 variants and FKBP5 in teenage suicide-completers.
Published: February, 2023

Abstract: A dysregulated hypothalamic-pituitary-adrenal (HPA) axis has repeatedly been demonstrated to play a fundamental role in psychiatric disorders and suicide, yet the mechanisms underlying this dysregulation are not clear. Decreased expression of the ...
Read more »

Bridging biological cfDNA features and machine learning approaches.
Published: February, 2023

Abstract: Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of ce...
Read more »

Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays
Published: February, 2023

Abstract: Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role...
Read more »

The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomol...
Read more »

The genome sequence of the common green Tenthredo, Tenthredo mesomela (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Tenthredo mesomela (the common green Tenthredo; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 393 megabases in span. Most of the assembly is scaffolded into 10 chro...
Read more »

A highly contiguous genome assembly for the California quail (Callipepla californica).
Published: February, 2023

Abstract: The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and O...
Read more »

The genome sequence of a bird blowfly, Protocalliphora azurea (Fallén,1817)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Protocalliphora azurea (a bird blowfly; Arthropoda; Insecta; Diptera; Calliphoridae). The genome sequence is 874 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseu...
Read more »

miR-34a and IRE1A/XBP-1(S) Form a Double-Negative Feedback Loop to Regulate Hypoxia-Induced EMT, Metastasis, Chemo-Resistance and Autophagy
Published: February, 2023

Abstract: Tumor-associated hypoxia, i.e., decreased availability of oxygen, results in a poor clinical outcome since it promotes EMT, metastasis, and chemotherapy-resistance. We have previously identified p53 and its target miR-34a, as critical determinants...
Read more »

The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal ps...
Read more »

The genome sequence of an ichneumonid wasp, Amblyteles armatorius (Forster, 1771)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Amblyteles armatorius (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 216 megabases in span. Most of the assembly is scaffolded into 12 chromosomal...
Read more »

The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseu...
Read more »

The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Agrotis puta (the Shuttle-shaped Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 522 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomo...
Read more »

Genome-wide DNA methylation analysis in an antimigraine-treated preclinical model of cortical spreading depolarization.
Published: February, 2023

Abstract: BACKGROUND: Cortical spreading depolarization, the cause of migraine aura, is a short-lasting depolarization wave that moves across the brain cortex, transiently suppressing neuronal activity. Prophylactic treatments for migraine, such as topirama...
Read more »

The genome sequence of the Forest Cuckoo Bee, Bombus sylvestris (Lepeletier, 1832)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Bombus sylvestris (the Forest Cuckoo Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence is 303 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomo...
Read more »

The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolec...
Read more »

The genome sequence of the starlet sea anemone, Nematostella vectensis (Stephenson, 1935)
Published: February, 2023

Abstract: We present a genome assembly from an individual Nematostella vectensis (the starlet sea anemone; Cnidaria; Anthozoa; Actiniaria; Edwardsiidae). The genome sequence is 269.4 megabases in span. Most of the assembly is scaffolded into 15 chromosomal ...
Read more »

The genome sequence of the lesser worm flesh fly, Sarcophaga (Sarcophaga) subvicina (Baranov, 1937)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Sarcophaga subvicina (the lesser worm flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 71 megabases in span. Most of the assembly (95.91\%) is scaffolded into six ...
Read more »

Temporal modification of H3K9/14ac and H3K4me3 histone marks mediates mechano-responsive gene expression during the accommodation process in poplar
Published: February, 2023

Abstract: Plants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent ...
Read more »

ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions
Published: February, 2023

Abstract: Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is r...
Read more »

T-toxin virulence genes: unconnected dots in a sea of repeats
Published: February, 2023

Abstract: In 1970, the Southern Corn Leaf Blight epidemic ravaged US fields to great economic loss. The outbreak was caused by never-before-seen, super-virulent, Race T of the fungus Cochliobolus heterostrophus. The functional difference between Race T and ...
Read more »

The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudo...
Read more »

The genome sequence of the cinnamon sedge caddisfly, Limnephilus marmoratus (Curtis, 1834)
Published: February, 2023

Abstract: We present a genome assembly from an individual Limnephilus marmoratus (a caddisfly; Arthropoda; Insecta; Trichoptera; Limnephilidae). The genome sequence is 1,630 megabases in span. Most of the assembly (99.93\%) is scaffolded into 30 chromosomal...
Read more »

The genome sequence of the pied hoverfly, Scaeva pyrastri (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Scaeva pyrastri (the pied hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 320 megabases in span. Most of the assembly is scaffolded into four chromosomal pseudomolec...
Read more »

The genome sequence of the Field Cuckoo-bee, Bombus campestris (Panzer, 1801)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Bombus campestris (the Field Cuckoo-bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence is 275 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomol...
Read more »

The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Ochlodes sylvanus, the Large Skipper (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 380 megabases in span. Most of the assembly (99.97\%) is scaffolded into 30 chromos...
Read more »

The genome sequence of the Coronet, Craniophora ligustri (Denis and Schiffermüller, 1775)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Craniophora ligustri (the Coronet; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 438 megabases in span. The whole assembly is scaffolded into 32 chromosomal pseudomolecu...
Read more »

A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain
Published: February, 2023

Abstract: We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three c...
Read more »

DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene.
Published: February, 2023

Abstract: Current chemical testing strategies are limited in their ability to detect non-genotoxic carcinogens (NGTxC). Epigenetic anomalies develop during carcinogenesis regardless of whether the molecular initiating event is associated with genotoxic (GTx...
Read more »

The genome sequence of the Brown Scallop, Philereme vetulata (Denis and Schiffermüller, 1775)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Philereme vetulata (the Brown Scallop; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 771 megabases in span. Most of the assembly is scaffolded into 68 chromosomal pseu...
Read more »

The genome sequence of the pale Rhogogaster, Rhogogaster chlorosoma (Benson, 1943)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Rhogogaster chlorosoma (the pale Rhogogaster; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 255 megabases in span. The whole assembly is scaffolded into 10 chromoso...
Read more »

The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomol...
Read more »

The genome sequence of a bluebottle, Calliphora vomitoria (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Calliphora vomitoria (a bluebottle; Arthropoda; Insecta; Diptera; Calliphoridae). The genome sequence is 708 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomole...
Read more »

The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Zeuzera pyrina (the Leopard Moth, Arthropoda; Insecta; Lepidoptera; Cossidae). The genome sequence is 687 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecule...
Read more »

The genome sequence of the Yellow-line Quaker, Agrochola macilenta (Hubner, 1809)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Agrochola macilenta (the Yellow-line Quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 683 megabases in span. Most of the assembly is scaffolded into 32 chromosomal ...
Read more »

The genome sequence of the Twin-spot Plume, Stenoptilia bipunctidactyla (Scopoli, 1763)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Stenoptilia bipunctidactyla (the Twin-spot Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 822.9 megabases in span. Most of the assembly is scaffolded into 30 chr...
Read more »

The genome sequence of the Common Snout Hoverfly, Rhingia campestris (Meigen, 1822)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Rhingia campestris (the Common Snout Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 720 megabases in span. Most of the assembly is scaffolded into five chromosomal ps...
Read more »

The genome sequence of the Mottled Sedge, Glyphotaelius pellucidus (Retzius, 1783)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Glyphotaelius pellucidus (Mottled Sedge, Arthropoda; Insecta; Trichoptera; Limnephilidae). The genome sequence is 1,037.1 megabases in span. Most of the assembly is scaffolded into 30 chromosoma...
Read more »

The genome sequence of the Small Ranunculus, Hecatera dysodea (Denis \& Schiffermüller, 1775)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Hecatera dysodea (the Small Ranunculus; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 640.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pse...
Read more »

The genome sequence of the Common Plume moth, Emmelina monodactyla (Linnaeus, 1758)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Emmelina monodactyla (the Common Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 312 megabases in span. Most of the assembly is scaffolded into 30 chromosomal p...
Read more »

Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation
Published: February, 2023

Abstract: Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. How...
Read more »

The genome sequence of the marsh skullcap, Scutellaria galericulata L.
Published: February, 2023

Abstract: We present a genome assembly from an individual Scutellaria galericulata (the marsh skullcap; Streptophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence is 328 megabases in span. Most of the assembly is scaffolded into 15 chromosomal p...
Read more »

The genome sequence of the Marmalade Hoverfly, Episyrphus balteatus (De Geer, 1776)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Episyrphus balteatus (the Marmalade Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 535 megabases in span. Most of the assembly is scaffolded into five chromosomal p...
Read more »

The genome sequence of the crab hacker barnacle, Sacculina carcini (Thompson, 1836)
Published: February, 2023

Abstract: We present a genome assembly from an individual female Sacculina carcini (crab hacker barnacle; Arthropoda; Crustacea; Thecostraca; Sacculinidae). The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into 28 chromosomal...
Read more »

Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Published: February, 2023

Abstract: As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome sc...
Read more »

MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression
Published: February, 2023

Abstract: Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which ...
Read more »

The genome sequence of the black needle fly, Leuctra nigra (Olivier, 1811)
Published: February, 2023

Abstract: We present a genome assembly from an individual male Leuctra nigra (black needle fly; Arthropoda; Insecta; Plecoptera; Leuctridae). The genome sequence is 536.3 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecu...
Read more »

The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecule...
Read more »

The genome sequence of the Brick, Agrochola circellaris (Hufnagel, 1766)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Agrochola circellaris (the Brick; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 572 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecul...
Read more »

The genome of Roselle's flesh fly Sarcophaga (Helicophagella) rosellei (Böttcher, 1912)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Sarcophaga rosellei (Roselle's flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into six chromosomal pseu...
Read more »

The genome sequence of the common green furrow bee, Lasioglossum morio (Fabricius, 1793)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Lasioglossum morio (the common green furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 547 megabases in span. Over half of the assembly (55.79\%) is scaffolded in...
Read more »

The genome sequence of a caddisfly, Limnephilus lunatus (Curtis, 1834)
Published: January, 2023

Abstract: We present a genome assembly from an individual Limnephilus lunatus (a caddisfly; Arthropoda; Insecta; Trichoptera; Limnephilidae). The genome sequence is 1,270 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecu...
Read more »

The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960)
Published: January, 2023

Abstract: We present a genome assembly from a Bugulina stolonifera colony (an erect bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence is 235 megabases in span. Most of the assembly (99.85\%) is scaffolded into 11 chromosomal ...
Read more »

The genome sequence of the Dimorphic Bear Hoverfly, Criorhina berberina (Fabricius, 1805)
Published: January, 2023

Abstract: We present a genome assembly from an individual female Criorhina berberina (the Dimorphic Bear Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 410 megabases in span. Most of the assembly (99.72\%) is scaffolded into four...
Read more »

Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B.
Published: January, 2023

Abstract: DNA methylation is a repressive epigenetic modification that is essential for development, exemplified by the embryonic and perinatal lethality observed in mice lacking de novo DNA methyltransferases (DNMTs). Here we characterise the role for DNMT...
Read more »

Neonatal inflammation increases hippocampal KCC2 expression through methylation-mediated TGF-β1 downregulation leading to impaired hippocampal cognitive function and synaptic plasticity in adult mice.
Published: January, 2023

Abstract: The mechanisms by which neonatal inflammation leads to cognitive deficits in adulthood remain poorly understood. Inhibitory GABAergic synaptic transmission plays a vital role in controlling learning, memory and synaptic plasticity. Since early-lif...
Read more »

Epigenomic charting and functional annotation of risk loci in renal cell carcinoma.
Published: January, 2023

Abstract: While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-...
Read more »

Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’
Published: January, 2023

Abstract: Background ‘Chambourcin’ is a French-American interspecific hybrid grape variety grown in the eastern and midwestern United States and used for making wine. Currently, there are few genomic resources available for hybrid grapevines like ‘Chambourc...
Read more »

The genome sequence of a snail-killing fly, Pherbina coryleti (Scopoli, 1763)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Pherbina coryleti (snail-killing fly; Arthropoda; Insecta; Diptera; Sciomyzidae). The genome sequence is 863 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomole...
Read more »

The genome sequence of the Pied Smudge, Ypsolopha sequella (Clerck, 1759)
Published: January, 2023

Abstract: We present a genome assembly from an individual Ypsolopha sequella (the Pied Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 867 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecu...
Read more »

The genome sequence of the segmented worm, Sthenelais limicola (Ehlers, 1864)
Published: January, 2023

Abstract: We present a genome assembly from an individual Sthenelais limicola (the segmented worm; Annelida; Polychaeta; Phyllodocida; Sigalionidae). The genome sequence is 1,131 megabases in span. Most of the assembly is scaffolded into nine chromosomal ps...
Read more »

The genome sequence of the sea mat, Membranipora membranacea (Linnaeus, 1767)
Published: January, 2023

Abstract: We present a genome assembly from an adult colony of Membranipora membranacea (the sea mat; Bryozoa; Gymnolaemata; Cheilostomatida; Membraniporidae). The genome sequence is 339 megabases in span. Most of the assembly (99.95\%) is scaffolded into 1...
Read more »

Opposing Effects of Interleukin-36γ and Interleukin-38 on Trained Immunity.
Published: January, 2023

Abstract: Trained immunity is the process of long-term functional reprogramming (a innate immune memory) of innate immune cells such as monocytes and macrophages after an exposure to pathogens, vaccines, or their ligands. The induction of trained immunity ...
Read more »

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation.
Published: January, 2023

Abstract: BACKGROUND: CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains...
Read more »

Whole-genome analysis of gamma-aminobutyric acid producing Psychobiotic Limosilactobacillus reuteri with its Untargeted metabolomics using UHPLC-Q-Tof MS/MS.
Published: January, 2023

Abstract: The gamma amino butyric acid (GABA) is a chemical messenger and is essential for the health of the brain and muscles. Some lactic acid bacteria (LAB) have the potential to function as psychobiotic cultures because they can produce significant amou...
Read more »

Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead.
Published: January, 2023

Abstract: Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead () and the Endan...
Read more »

Physiological reprogramming in vivo mediated by Sox4 pioneer factor activity
Published: January, 2023

Abstract: Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors media...
Read more »

The age of bone marrow dictates the clonality of smooth muscle-derived cells in atherosclerotic plaques.
Published: January, 2023

Abstract: Aging is the predominant risk factor for atherosclerosis, the leading cause of death. Rare smooth muscle cell (SMC) progenitors clonally expand giving rise to up to ~70\% of atherosclerotic plaque cells; however, the effect of age on SMC clonality...
Read more »

Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.
Published: January, 2023

Abstract: Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki fragment sequencing (OK-seq), a quantitati...
Read more »

Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode.
Published: January, 2023

Abstract: Laportea bulbifera, a Miao medicine grown in karst areas, has exerted a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. ...
Read more »

Intraperitoneal 5-Azacytidine Alleviates Nerve Injury-Induced Pain in Rats by Modulating DNA Methylation.
Published: January, 2023

Abstract: To investigate the role of DNA methylation in modulating chronic neuropathic pain (NPP), identify possible target genes of DNA methylation involved in this process, and preliminarily confirm the medicinal value of the DNA methyltransferases (DNMTs...
Read more »

Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies
Published: January, 2023

Abstract: Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomp...
Read more »

Impact of Fetal Exposure to Endocrine Disrupting Chemical Mixtures on FOXA3 Gene and Protein Expression in Adult Rat Testes.
Published: January, 2023

Abstract: Perinatal exposure to endocrine disrupting chemicals (EDCs) has been shown to affect male reproductive functions. However, the effects on male reproduction of exposure to EDC mixtures at doses relevant to humans have not been fully characterized. ...
Read more »

The aryl hydrocarbon receptor cell intrinsically promotes resident memory CD8 T cell differentiation and function.
Published: January, 2023

Abstract: The Aryl hydrocarbon receptor (Ahr) regulates the differentiation and function of CD4 T cells; however, its cell-intrinsic role in CD8 T cells remains elusive. Herein we show that Ahr acts as a promoter of resident memory CD8 T cell (T) differenti...
Read more »

The genome sequence of the White-barred Gold, Micropterix aruncella (Scopoli, 1763)
Published: January, 2023

Abstract: We present a genome assembly from an individual female Micropterix aruncella (the White-barred Gold; Arthropoda, Insecta, Lepidoptera; Micropterigidae). The genome sequence is 1,079 megabases in span. Most of the assembly is scaffolded into 31 chr...
Read more »

The genome sequence of the dark-saddled leucozona, Leucozona laternaria (Muller, 1776)
Published: January, 2023

Abstract: We present a genome assembly from an individual female Leucozona laternaria (the dark-saddled leucozona; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 614 megabases in span. Most of the assembly (99.69\%) is scaffolded into five...
Read more »

The genome sequence of the spotted kaleidoscope jellyfish, Haliclystus octoradiatus (James-Clark, 1863)
Published: January, 2023

Abstract: We present a genome assembly from an individual Haliclystus octoradiatus (the spotted kaleidoscope jellyfish; Cnidaria; Staurozoa; Stauromedusae; Haliclystidae). The genome sequence is 262 megabases in span. Most of the assembly (98.3\%) is scaffo...
Read more »

The genome sequence of the ichneumon wasp Buathra laborator (Thunberg, 1822)
Published: January, 2023

Abstract: We present a genome assembly from an individual Buathra laborator (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 330 megabases in span. Over 60\% of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mit...
Read more »

Human ERG oncoprotein represses a Drosophila LIM domain bindingprotein–coding gene Chip
Published: January, 2023

Abstract: Human TS elated ene, ERG, a master transcription factor, turns oncogenic upon its out-of-context activation in diverse developmental lineages. However, the mechanism underlying its lineage-specific activation of Notch (N), Wnt, or EZH2-three well-...
Read more »

DNA dioxygenases Tet2/3 regulate gene promoter accessibility and chromatin topology in lineage-specific loci to control epithelial differentiation.
Published: January, 2023

Abstract: Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes, catalyzing 5-methylcytosine oxidation in DNA. Here, by using --driven ablation of ...
Read more »

A Systemic and Integrated Analysis of p63-Driven RegulatoryNetworks in Mouse Oral Squamous Cell Carcinoma.
Published: January, 2023

Abstract: Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of dis...
Read more »

The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Hypsopygia costalis (the Gold Triangle; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 818 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudom...
Read more »

The genome sequence of a ground beetle, Nebria brevicollis (Fabricius, 1792)
Published: January, 2023

Abstract: We present a genome assembly from an individual female Nebria brevicollis (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 242 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomol...
Read more »

Epigenetics and stroke: role of DNA methylation and effect of aging on blood-brain barrier recovery.
Published: January, 2023

Abstract: Incomplete recovery of blood-brain barrier (BBB) function contributes to stroke outcomes. How the BBB recovers after stroke remains largely unknown. Emerging evidence suggests that epigenetic factors play a significant role in regulating post-stro...
Read more »

Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep.
Published: January, 2023

Abstract: UNLABELLED: Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mec...
Read more »

The genome sequence of the Festoon, Apoda limacodes (Hufnagel, 1766)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Apoda limacodes (the Festoon; Arthropoda; Insecta; Lepidoptera; Limacodidae). The genome sequence is 800 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules...
Read more »

The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96\%) is scaffolded into 30...
Read more »

The genome sequence of the bluish flesh fly, Sarcophaga  (Robineauella) caerulescens (Zetterstedt, 1838)
Published: January, 2023

Abstract: We present a genome assembly from an individual male Sarcophaga caerulescens (the bluish flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 597 megabases in span. Most of the assembly is scaffolded into seven chromosom...
Read more »

Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS.
Published: January, 2023

Abstract: DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we deve...
Read more »

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse.
Published: January, 2023

Abstract: BACKGROUND: As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athle...
Read more »

Role of epigenetics in the etiology of hypospadias through penile foreskin DNA methylation alterations.
Published: January, 2023

Abstract: Abnormal penile foreskin development in hypospadias is the most frequent genital malformation in male children, which has increased dramatically in recent decades. A number of environmental factors have been shown to be associated with hypospadias...
Read more »

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Published: January, 2023

Abstract: Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Her...
Read more »

In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming
Published: January, 2023

Abstract: Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite duri...
Read more »

A chromosome-level reference genome and pangenome for barn swallow population genomics.
Published: January, 2023

Abstract: Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn sw...
Read more »

Utility of long-read sequencing for All of Us
Published: January, 2023

Abstract: The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compared the performance of traditional short-read sequ...
Read more »

The genome sequence of thale cress, Arabidopsis thaliana (Heynh., 1842)
Published: January, 2023

Abstract: We present a genome assembly of an Arabidopsis thaliana specimen (thale cress; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence spans 138 megabases. Most of the assembly (98.76\%) is scaffolded into five chromosomal pse...
Read more »

The genome sequence of the plain dark bee, Stelis phaeoptera (Kirby, 1802)
Published: January, 2023

Abstract: We present a genome assembly from an individual female Stelis phaeoptera (the plain dark bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 301 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pse...
Read more »

Gene Regulatory Interactions at Lamina-Associated Domains
Published: January, 2023

Abstract: The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How the...
Read more »

The genome sequence of the turban top shell, Gibbula magus (Linnaeus, 1758)
Published: January, 2023

Abstract: We present a genome assembly from an individual Gibbula magus (the turban top shell; Mollusca; Gastropoda; Trochida; Trochidae). The genome sequence is 1,470 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules...
Read more »

CD8 CD226 T cells in liver metastases dictate the prognosis of colorectal cancer patients treated with chemotherapy and radical surgery.
Published: January, 2023

Abstract: CD226 has been reported to participate in the rescue of CD8 T cell dysfunction. In this study, we aimed to assess the prognostic value of CD226 in tumor-infiltrating lymphocytes (TILs) derived from colorectal cancer (CRC) liver metastases treated ...
Read more »

The genome sequence of the Kent black arches, Meganola albula (Denis \& Schiffermüller, 1775)
Published: December, 2022

Abstract: We present a genome assembly from an individual male Meganola albula (the Kent black arches; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 405 megabases in span. Most of the assembly (99.95\%) is scaffolded into 30 chromosomal...
Read more »

The genome sequence of the dotted bee-fly, Bombylius discolor (Mikan, 1796)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Bombylius discolor (the dotted bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 280 megabases in span. Most of the assembly (99.93\%) is scaffolded into six chromoso...
Read more »

The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758)
Published: December, 2022

Abstract: We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100\%) is scaffolded into 23 chromosomal ps...
Read more »

The genome sequence of the cave orb-weaver, Meta bourneti (Simon, 1922)
Published: December, 2022

Abstract: We present a genome assembly from an individual male Meta bourneti (the cave orb-weaver; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 1,383 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudo...
Read more »

The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudom...
Read more »

The genome sequence of the scale worm, Lepidonotus clava (Montagu, 1808)
Published: December, 2022

Abstract: We present a genome assembly from an individual Lepidonotus clava (scale worm; Annelida; Polychaeta; Phyllodocida; Polynoidae). The genome sequence is 1,044 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules....
Read more »

The genome sequence of the early grey, Xylocampa areola (Esper, 1789)
Published: December, 2022

Abstract: We present a genome assembly from an individual Xylocampa areola (the early grey; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, i...
Read more »

The genome sequence of the northern brown argus, Aricia artaxerxes (Fabricius, 1793)
Published: December, 2022

Abstract: We present a genome assembly from an individual Aricia artaxerxes (the northern brown argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 458 megabases in span. Most of the assembly (99.99\%) is scaffolded into 23 chromoso...
Read more »

Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.
Published: December, 2022

Abstract: Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference g...
Read more »

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.
Published: December, 2022

Abstract: BACKGROUND: The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization play...
Read more »

Species-specific basecallers improve actual accuracy of nanopore sequencing in plants.
Published: December, 2022

Abstract: BACKGROUND: Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is ...
Read more »

The genome sequence of the lesser treble-bar moth, Aplocera efformata (Guenée, 1857)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Aplocera efformata (the lesser treble-bar; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 349.5 megabases in span. Most of the assembly (99.97\%) is scaffolded into 32 ...
Read more »

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae.
Published: December, 2022

Abstract: Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemis...
Read more »

The genome sequence of the common grass-veneer, Agriphila tristella (Denis \& Schiffermüller, 1775)
Published: December, 2022

Abstract: We present a genome assembly from an individual male Agriphila tristella (the common grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 802 megabases in span. Most of the assembly (99.83\%) is scaffolded into 23 chr...
Read more »

546. European project AQUA-FAANG: the epigenetic landscape of the Atlantic Salmon; focus on liver tissue
Published: December, 2022

Abstract: As part of the European project AQUA-FAANG, we produced a body map of the epigenetic and regulatory landscape of Atlantic salmon, spanning different tissues in both sexes and at two stages of maturity. For this purpose, we developed and applied re...
Read more »

The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis \& Schiffermüller, 1775)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98\%) is scaffolded into 29...
Read more »

The genome sequence of the common mini-mining bee Andrena minutula (Kirby, 1802)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Andrena minutula (the common mini-mining bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 380 megabases in span. Most of the assembly (92.19\%) is scaffolded into sev...
Read more »

The genome sequence of the white admiral, Limenitis camilla (Linnaeus, 1764)
Published: December, 2022

Abstract: We present a genome assembly from an individual female Limenitis camilla (the white admiral; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 435 megabases in span. Most of the assembly (99.97\%) is scaffolded into 31 chromos...
Read more »

The genome sequence of the apple, Malus domestica (Suckow) Borkh., 1803
Published: December, 2022

Abstract: We present genome assemblies from four Malus domestica cultivars (the apple; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequences are 643–653 megabases in span. The greater part of each assembly length (99.24–99.74\%) is scaffolde...
Read more »

The genome sequence of the European crab apple, Malus sylvestris (L.) Mill., 1768
Published: December, 2022

Abstract: We present a genome assembly from an individual Malus sylvestris (the European or 'wild' crab apple; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 642 megabases in span. Most of the assembly (99.98\%) is scaffolded into 1...
Read more »

Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets.
Published: December, 2022

Abstract: Variant callers typically produce massive numbers of false positives for structural variations, such as cancer-relevant copy-number alterations and fusion genes resulting from genome rearrangements. Here we describe an ultrafast and accurate detec...
Read more »

Trichoderma root colonization triggers epigenetic changes in jasmonic and salicylic acid pathway-related genes.
Published: December, 2022

Abstract: Beneficial interactions between plant-roots and Trichoderma spp. lead to a local and systemic enhancement of the plant immune system through a mechanism known as priming of defenses. In recent reports, we outlined a repertoire of genes and protein...
Read more »

Intranasal administration of Acinetobacter lwoffii in a murine model of asthma induces IL-6-mediated protection associated with cecal microbiota changes.
Published: December, 2022

Abstract: BACKGROUND: Early-life exposure to certain environmental bacteria including Acinetobacter lwoffii (AL) has been implicated in protection from chronic inflammatory diseases including asthma later in life. However, the underlying mechanisms at the i...
Read more »

Genome surveillance by HUSH-mediated silencing of intronless mobile elements.
Published: January, 2022

Abstract: All life forms defend their genome against DNA invasion. Eukaryotic cells recognize incoming DNA and limit its transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long inters...
Read more »

From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions
Published: December, -1

Abstract: Introduction In the progressive phase of multiple sclerosis (MS), the hampered differentiation capacity of oligodendrocyte precursor cells (OPCs) eventually results in remyelination failure. We have previously shown that DNA methylation of Id2/Id4...
Read more »

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade
Published: December, -1

Abstract: Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are mostly unknown but can rely on the ability to release phytoh...
Read more »

ニュース

 すべてのニュースを見る


The European Regional Development Fund and Wallonia are investing in your future.

Extension of industrial buildings and new laboratories.


       Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics