Diagenode

Newly added

117 publications found.

A transgenic mice model of retinopathy of cblG-type inherited disorder of one-carbon metabolism highlights epigenome-wide alterations related to cone photoreceptor cells development and retinal metabolism.
Published: October, 2023

Abstract: BACKGROUND: MTR gene encodes the cytoplasmic enzyme methionine synthase, which plays a pivotal role in the methionine cycle of one-carbon metabolism. This cycle holds a significant importance in generating S-adenosylmethionine (SAM) and S-adenosyl...
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G-quadruplexes of KSHV oriLyt play important roles in promoting lytic DNA replication.
Published: October, 2023

Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes distinct origins of DNA replication (origin of replications) during the latent and lytic phases of its life cycle. Lytic DNA replication requires the participation of cellular and viral prote...
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FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells
Published: August, 2023

Abstract: Background The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or...
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Nuclear proinflammatory cytokine S100A9 enhances expression of human papillomavirus oncogenes via transcription factor TEAD1.
Published: August, 2023

Abstract: Transcription of the human papillomavirus (HPV) oncogenes, and , is regulated by the long control region (LCR) of the viral genome. Although various transcription factors have been reported to bind to the LCR, little is known about the transcript...
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A high-throughput screening assay for silencing established HIV-1 macrophage infection identifies nucleoside analogs that perturb H3K9me3 on proviral genomes.
Published: August, 2023

Abstract: HIV-infected macrophages are long-lived cells that represent a barrier to functional cure. Additionally, low-level viral expression by central nervous system (CNS) macrophages contributes to neurocognitive deficits that develop despite antiretrovi...
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Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells.
Published: July, 2023

Abstract: The Zfp296 gene encodes a zinc finger-type protein. Its expression is high in mouse embryonic stem cells (ESCs) but rapidly decreases following differentiation. Zfp296-knockout (KO) ESCs grew as flat colonies, which were reverted to rounded coloni...
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Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells.
Published: July, 2023

Abstract: Isocitrate dehydrogenase (IDH) mutations are found in 20\% of acute myeloid leukemia (AML) patients. However, only 30-40\% of the patients respond to IDH inhibitors (IDHi). We aimed to identify a molecular vulnerability to tailor novel therapies f...
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The NF-Y splicing signature controls hybrid EMT and ECM-related pathways to promote aggressiveness of colon cancer.
Published: June, 2023

Abstract: Aberrant splicing events are associated with colorectal cancer (CRC) and provide new opportunities for tumor diagnosis and treatment. The expression of the splice variants of NF-YA, the DNA binding subunit of the transcription factor NF-Y, is dere...
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Effect of Aerobic/Strength Training on RANKL Gene DNA Methylation Levels.
Published: June, 2023

Abstract: BACKGROUND: The osteoclastogenesis RANKL gene plays a key role in bone remodeling. The hypomethylation of its promoter region may cause osteoporosis. The present study aimed to elucidate the influence of physical activity on DNA methylation change...
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A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni.
Published: March, 2023

Abstract: BACKGROUND: Biomphalaria pfeifferi is the world's most widely distributed and commonly implicated vector snail species for the causative agent of human intestinal schistosomiasis, Schistosoma mansoni. In efforts to control S. mansoni transmission,...
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The genome sequence of the Lime-speck Pug, Eupithecia centaureata (Denis \& Schiffermüller, 1775)
Published: March, 2023

Abstract: We present a genome assembly from an individual male Eupithecia centaureata (the Lime-speck Pug; Arthropoda; Insect; Lepidoptera; Geometridae). The genome sequence is 465.6 megabases in span. Most of the assembly is scaffolded into 32 chromosomal ...
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The genome sequence of the Early Bumblebee, Bombus pratorum (Linnaeus, 1761)
Published: March, 2023

Abstract: We present a genome assembly from an individual female Bombus pratorum (the Early Bumblebee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence is 285.1 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomo...
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The genome sequence of the Golden-tailed Leafwalker, Xylota sylvarum (Linnaeus, 1758)
Published: March, 2023

Abstract: We present a genome assembly from an individual male Xylota sylvarum (the Golden-tailed Leafwalker; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 534.8 megabases in span. Most of the assembly is scaffolded into five chromosomal ...
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A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus).
Published: March, 2023

Abstract: The Lesser Prairie-Chicken (Tympanuchus pallidicinctus; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays. Unfortunately, the species has disappeared across much of its historical range,...
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The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758)
Published: March, 2023

Abstract: We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseud...
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The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825)
Published: March, 2023

Abstract: We present a genome assembly from an individual male Apotomis turbidana (the White-shouldered Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 720.5 megabases in span. Most of the assembly is scaffolded into 28 chromo...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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 ...
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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 ...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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. ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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....
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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...
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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...
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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...
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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...
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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 ...
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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 ...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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A genome-wide screen reveals new regulators of the 2-cell-like cell state
Published: June, 2022

Abstract: In mammals, only the zygote and blastomeres of the early embryo are fully totipotent. This totipotency is mirrored in vitro by mouse "2-cell-like cells" (2CLCs), which appear at low frequency in cultures of Embryonic Stem cells (ESCs). Because tot...
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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...
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