71 results match your criteria novaseq 6000


Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China.

Gut Pathog 2021 Oct 13;13(1):59. Epub 2021 Oct 13.

Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.

Background: To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.

Methods: Four Citrobacter spp. Read More

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October 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail.

Genomics Inform 2021 Sep 30;19(3):e32. Epub 2021 Sep 30.

Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Read More

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September 2021

Complete Genome Sequence of a Clinical Isolate of Acinetobacter baumannii Harboring 11 Plasmids.

Microbiol Resour Announc 2021 Sep 30;10(39):e0069521. Epub 2021 Sep 30.

Department of Bacteriology, Graduate School of Medicine, Osaka City University, Abeno, Osaka, Japan.

Here, we report the complete genome sequence of an Acinetobacter baumannii isolate harboring 11 plasmids, obtained at a hospital in Japan in 2016. The complete 4.07-Mbp genome sequence (1 chromosome and 11 plasmids) was analyzed by a combination of long-read (Flongle) and short-read (NovaSeq 6000) sequencing. Read More

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September 2021

The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold.

Mol Biol Rep 2021 Sep 19. Epub 2021 Sep 19.

School of Business and Trade, Nanjing Vocational University of Industry Technology, Nanjing, 210046, China.

Background: An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. Read More

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September 2021

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.

Nat Biotechnol 2021 09 9;39(9):1129-1140. Epub 2021 Sep 9.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. Read More

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September 2021

Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages.

BMC Genomics 2021 Sep 3;22(1):637. Epub 2021 Sep 3.

Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO, USA.

Background: The pond snail, Lymnaea stagnalis (L. stagnalis), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. Read More

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September 2021

Emergence and Genetic Characterization of Plasmid-Encoded VIM-2-Producing with Novel Integron In Isolated from Cerebrospinal Fluid.

Infect Drug Resist 2021 24;14:3415-3424. Epub 2021 Aug 24.

Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.

Purpose: To investigate the genomic and plasmid characteristics of a newly discovered strain with a -carrying plasmid and novel integron In isolated from a cerebrospinal fluid specimen in a teaching hospital.

Methods: Species identification was performed by MALDI-TOF MS, and was identified by PCR and Sanger sequencing. Whole-genome sequencing analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Read More

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Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19.

Elife 2021 08 13;10. Epub 2021 Aug 13.

HUMANOID CoRE, University of California San Diego, San Diego, United States.

Background: SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear.

Methods: We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Read More

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First Report of Turnip Mosaic Virus in Peanut (Arachis hypogaea L.) in China.

Plant Dis 2021 Aug 29. Epub 2021 Aug 29.

Ningbo University, 47862, State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Fenghua Road 818, Ningbo, China, 315211;

Peanut (Arachis hypogaea L.) is an important source of edible oil in China but its yield and quality in agricultural production are affected by a number of diseases including those caused by viruses. The four viruses most commonly reported to affect the production of peanut worldwide are peanut stripe virus, cucumber mosaic virus, peanut stunt virus and peanut bud necrosis virus (Srinivasan et al. Read More

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Sequencing and de Novo Assembly of Abaca ( Née) var. Abuab Genome.

Genes (Basel) 2021 Aug 2;12(8). Epub 2021 Aug 2.

Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville, MD 20705, USA.

Abaca ( Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Read More

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"More Guts Than Brains?"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension.

J Neuroophthalmol 2021 Jul 13. Epub 2021 Jul 13.

Department of Ophthalmology (EB, BT, AK), Hillel Yaffe Medical Center, Hadera, Israel; Institute of Gastroenterology and Hepatology (YK), Hillel Yaffe Medical Center, Hadera, Israel; Department of Cell Biology and Cancer Science (DK, SC, NG-K), Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, Israel; Sackler Faculty of Medicine (AK), Tel Aviv University, Tel Aviv, Israel; and Canadian Institute for Advanced Research (CIFAR) (NG-Z), Azrieli Global Scholar, MaRS Centre, Toronto, Canada.

Background: Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Read More

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Structural and Functional Impacts of Microbiota on and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea.

Microorganisms 2021 Jun 12;9(6). Epub 2021 Jun 12.

Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples ( = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Read More

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Examination of the Transcriptional Response to Overexpression in (Lamb.) Carr.

Biology (Basel) 2021 Jun 23;10(7). Epub 2021 Jun 23.

State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.

The study of somatic embryogenesis can provide insight into early plant development. We previously obtained -overexpressing embryonic cell lines of (Lamb.) Carr. Read More

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Characterization of the complete mitochondrial genome of , a wild saprobic mushroom in China.

Mitochondrial DNA B Resour 2021 Jun 14;6(7):1979-1981. Epub 2021 Jun 14.

College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China.

The Glistening Inkcap () is a wild saprobic mushroom in China. In this study, we assembled and annotated its complete mitochondrial genome using raw data sequenced through Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). The length of the . Read More

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Small RNA Sequencing of Aqueous Humor and Plasma in Patients With Primary Open-Angle Glaucoma.

Invest Ophthalmol Vis Sci 2021 06;62(7):24

University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht, The Netherlands.

Purpose: Identify differentially expressed microRNAs (miRNAs) in aqueous humor (AH) and blood of primary open-angle glaucoma (POAG) patients by using small RNA sequencing. These may provide insight into POAG pathophysiology or serve as diagnostic biomarker.

Methods: AH and plasma of nine POAG patients and 10 cataract control patients were small RNA sequenced on Illumina NovaSeq 6000. Read More

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Coexistence of two bla genes in a bla-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China.

J Glob Antimicrob Resist 2021 Sep 21;26:11-14. Epub 2021 May 21.

Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China. Electronic address:

Objectives: The emergence of carbapenem-resistant Enterobacteriaceae has become a serious public-health threat. Here we report the complete genome sequence of a multidrug-resistant (MDR) Escherichia coli carrying bla and two copies of bla recovered from a bloodstream infection in China.

Methods: Whole-genome sequencing of E. Read More

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September 2021

Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents.

Sci Rep 2021 05 13;11(1):10188. Epub 2021 May 13.

The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai - Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai, 200031, China.

Arenaviruses represent a family of viruses that are naturally present in rodents belonging to subfamily Murinae, Neotominae or Sigmodontinae. Except for Lassa virus, little information is available on other Old-World arenaviruses. Here, we describe strain AnRB3214, a virus isolated from a presumed Praomys sp. Read More

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The Illumina Sequencing Protocol and the NovaSeq 6000 System.

Methods Mol Biol 2021 ;2242:15-42

Department of Biology, University of Firenze, Firenze, Italy.

The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Read More

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Gynura japonica: A new host of Apple stem grooving virus and Chrysanthemum virus B in China.

Plant Dis 2021 Apr 28. Epub 2021 Apr 28.

Ningbo University, 47862, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo, Zhejiang, China;

Gynura japonica (Thunb.) Juel [Asteraceae; syn: G. segetum (Lour. Read More

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Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook.

Phytochemistry 2021 Jul 16;187:112772. Epub 2021 Apr 16.

Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India. Electronic address:

Fritillaria roylei Hook. is a critically endangered high altitude Himalayan medicinal plant species with rich source of pharmaceutically active structurally diverse steroidal alkaloids. Nevertheless, except few marker compounds, the chemistry of the plant remains unexplored. Read More

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Comparison between MGI and Illumina sequencing platforms for whole genome sequencing.

Genes Genomics 2021 Jul 17;43(7):713-724. Epub 2021 Apr 17.

Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea.

Background: Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencing instruments.

Objective: In this study, we compared the performance of the two platform's major sequencing instruments-Illumina's NovaSeq 6000 and MGI's MGISEQ-2000 and DNBSEQ-T7-to test whether the MGISEQ-2000 and DNBSEQ-T7 sequencing instruments are also suitable for whole genome sequencing. Read More

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Sequencing error profiles of Illumina sequencing instruments.

NAR Genom Bioinform 2021 Mar 27;3(1):lqab019. Epub 2021 Mar 27.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets. Read More

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The complete mitochondrial genome of Zhehuang-1 (Hymenochaetales, Basidiomycota).

Mitochondrial DNA B Resour 2021 Mar 19;6(3):1096-1097. Epub 2021 Mar 19.

Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, People's Republic of China.

In this study, the complete mitochondrial genome of Zhehuang-1 was determined. Genomic DNA samples individually collected from a population in southeastern China (Qiandaohu, Zhejiang Province, N29°44'24'', E118°52'48'') were sequenced with an Illumina NovaSeq 6000. The complete mitochondrial genome was 97,345 bp in length and consisted of 22 protein-coding genes (PCGs), 29 tRNAs, 3 ribosomal RNAs, and a control region. Read More

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From Turkey: First Report of KPC-3- and CTX-M-27-Producing Multidrug-Resistant ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations.

Microb Drug Resist 2021 Sep 31;27(9):1265-1270. Epub 2021 Mar 31.

Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gumushane University, Gümüşhane, Turkey.

The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant strain. Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Read More

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September 2021

Forecasting early onset diminished ovarian reserve for young reproductive age women.

J Assist Reprod Genet 2021 Jul 30;38(7):1853-1860. Epub 2021 Mar 30.

Colorado Center for Reproductive Medicine, Lone Tree, Colorado, 80124, USA.

Purpose: To investigate the biological networks associated with DOR in young women and the subsequent molecular impact on preimplantation embryos.

Methods: Whole peripheral blood was collected from patients: young women presenting with diminished ovarian reserve (DOR) and age-matched young women with normal ovarian reserve. Maternal exome sequencing was performed on the NovaSEQ 6000 and sequencing validation was completed using Taqman® SNP Genotyping Assays. Read More

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Genomic and phylogenetic analysis of multidrug-resistant Achromobacter xylosoxidans ST273 strain MTYH1 co-carrying bla and bla recovered from a wound infection in China.

J Glob Antimicrob Resist 2021 06 22;25:110-113. Epub 2021 Mar 22.

Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, China. Electronic address:

Objectives: Achromobacter xylosoxidans is widely distributed in the environment and is increasingly recognised as a significant nosocomial pathogen in healthcare settings. However, the genomic and phylogenetic characteristics of this pathogen are not fully understood. Here we report the first genome sequence of a multidrug-resistant A. Read More

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Transcriptome Assembly of Two Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids.

Int J Mol Sci 2021 Feb 19;22(4). Epub 2021 Feb 19.

Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea.

species produce a high amount of phytoecdysteroids (PEs), which are widely used in traditional medicine in the Pacific islands. The PEs in two different species, (MP) and (MS), were examined using high-performance liquid chromatography (HPLC). In particular, MS produces a high amount of 20-hydroxyecdysone, which is the main active compound in PEs. Read More

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February 2021

The complete chloroplast genome of a medical herb, Fisch. (Rosaceae), from Qinghai-Tibet Plateau in China.

Mitochondrial DNA B Resour 2021 Feb 8;6(2):349-350. Epub 2021 Feb 8.

The College of Biological Science, Qinghai Normal University, Xining, China.

Fisch. (Rosaceae) is one of the genuine medicinal materials in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of using Illumina NovaSeq 6000 platform. Read More

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February 2021

The complete mitochondrial genome of (Hypocreales: Cordycipitaceae).

Mitochondrial DNA B Resour 2021 Feb 12;6(2):586-588. Epub 2021 Feb 12.

College of Landscape and Art, Jiangxi Agricultural University, Nanchang, China.

The mitochondrial genome of , strain RCEF500, was sequenced on the NovaSeq 6000 and the Nanopore Sequencer, and annotated. The genome is 59,014 bp in length, encoding 15 conserved protein-coding genes (PCGs), 2 rRNA genes and 23 tRNA genes. The nucleotide composition of mitochondrial genome was 38. Read More

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February 2021

Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.).

Genomics 2021 May 16;113(3):910-918. Epub 2021 Feb 16.

UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia. Electronic address:

Weeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. Read More

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