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Frontiers | High-throughput sequencing reveals the presence of novel and known viruses in diseased Paris yunnanensis

Viral diseases of Paris spp. have become serious problems in cultivation of this group of important medicinal plants in China. In this study, eight viruses were identified in the diseased plants of Paris yunnanensis by high-throughput sequencing (HTS) and RT-PCR. These viruses include three novel viruses (two potyviruses and one nepovirus), Hippeastrum chlorotic ringspot virus (HCRV)，Lychnis mottle virus (LycMoV), Paris mosaic necrosis virus (PMNV), Paris virus 1 and pepper mild mottle virus. The three new viruses were tentatively named Paris potyvirus 3 (ParPV-3), Paris potyvirus 4 (ParPV-4), Paris nepovirus 1 (ParNV-1) and their complete genome sequences were determined. Sequence analyses showed ParPV-3 and ParPV-4 shared the highest amino acid (aa) sequence identities of 54.3% to each other and 53.0-57.8% to other known potyviruses. ParNV-1 had aa sequence identities of 28.8-63.7% at protease-polymerase (Pro-Pol) with other nepoviruses. Phylogenetic analyses further support that t ....

United States , France General , Potyviridae Adams , Potyvirus Chen , Betaflexiviridae Dong , Secoviridae Dullemans , Cucurbitaceae Xu , Paridis Rhizoma , Jacq Salisb , Vpg Pol , Potyvirus Yang , Virgaviridae Wen , Tobamovirus Chen , Secoviridae Thompson , Clustal Omega , National Science Foundation Of China , National Center , Greentaq Mix Vazyme Biotech Co Ltd , Chinese Medicine Resources Co Ltd , Takara Biotechnology Co , Chinese Academy Of Sciences , Clinx Science Instruments Co Ltd , Yunheng Ji Kunming Institute Of Botany , Origingene Bio Pharm Technology Co , Yunnan Baiyao , Chinese Pharmacopoeia ,

Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
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United States , Hong Kong , United Kingdom , Godfrey Hewitt , Marine Research , Genomics Institute , University Of St Andrews , Wellcome Trust , Marine Alliance For Science , Swiss National Science Foundation , University Of Groningen , Fisheries Science Center , Systematics Research Fund , University Of St Andrews Bioinformatics Unit , European Union Horizon , Wildlife Service , University Of St , People Trust For Endangered Species , American Museum Of Natural History , European Society For Evolutionary Biology , Technology For Scotland , North Atlantic , Southwest Fisheries Science Center , Supplementary Text , Beijing Genomics Institute , Illumina Hiseqx Ten ,

Epigenomic landscape and 3D genome structure in pediatric high-grade glioma

Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M , JAG2 , and FLRT1 . Together, our results imply three-dimensional genome a ....

Northwestern University , United States , Roberth Lurie , Kapa Biosystems , Library Preparation Kit , Cell Signaling Technology , Beckman Coulter , Bristol Myers Squibb , Empire Genomics , Institutional Review Board , Illumina Truseq Stranded Total , Illumina Nextseq , Santa Cruz Biotechnology , Preparation Kit , Bioo Scientific , Agilent High Sensitivity , Arima Genomics , Elute Polymerase Chain Reaction , Purification Kit , Illumina Hiseqx Ten , Thermo Fisher Scientific , Assay Kit , Tris Buffered Saline Tween , Mini Kit , Strand Synthesis System Kit , வடமேற்கு பல்கலைக்கழகம் ,