1,585 results match your criteria assembled whole-genome


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

High quality genome resource of mango bacterial black spot pathogen Xanthomonas citri pv. mangiferaeindicae GXG07 isolated from Guangxi, China.

Plant Dis 2021 Oct 11. Epub 2021 Oct 11.

Guangxi University, 12664, Nanning, Guangxi, China.

Xanthomonas citri pv. mangiferaeindicae (Xcm) is the causal agent of mango bacterial black spot which is present in many mango growing regions and leads to great economic losses to mango industry. Due to the limitation of high-quality genomic resources, little is known about the molecular pathogenesis of Xcm. Read More

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October 2021

The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development.

Plant J 2021 Oct 8. Epub 2021 Oct 8.

Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China.

Wintersweet (Chimonanthus praecox) is one of the most important ornamental plants, whose color is mainly determined by the middle tepals. However, the molecular mechanisms underlying the intriguing flower color development among different wintersweet groups are still largely unknown. In addition, wintersweet belongs to magnoliids, and the issue remains as to how to determine the phylogenetic position of magnoliids conclusively. Read More

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October 2021

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests.

Commun Biol 2021 Oct 7;4(1):1166. Epub 2021 Oct 7.

Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g. Read More

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October 2021

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.

Brief Bioinform 2021 Oct 8. Epub 2021 Oct 8.

School of Computer Science and Engineering, Central South University, China.

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. Read More

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October 2021

Whole Genome Sequence of , the Causal Agent of Black Spot of Kiwifruit.

Front Microbiol 2021 20;12:713462. Epub 2021 Sep 20.

College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China.

is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of (Y784-BC03) was isolated and identified from "Hongyang" kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. Read More

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September 2021

Genome of Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for .

Front Microbiol 2021 16;12:724451. Epub 2021 Sep 16.

International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China.

is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other species, wild can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Read More

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September 2021

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola.

BMC Genomics 2021 Oct 2;22(1):708. Epub 2021 Oct 2.

Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany.

Background: Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Read More

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October 2021

Characterisation of the whole genome sequence of an avian hepatitis E virus directly from clinical specimens reveals possible recombination events between European and USA strains.

Infect Genet Evol 2021 Sep 29;96:105095. Epub 2021 Sep 29.

Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia.

Avian hepatitis E virus (aHEV) is the causative agent of an important disease of broiler breeders and layers. aHEV cannot be readily propagated in cell culture and is characterised primarily by sequencing of amplicons generated through several RT-PCRs that target individual genes. This study aims to uncover the origin of current Australian aHEV isolates based on whole genome sequencing using clinical liver tissues. Read More

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September 2021

Complete genome sequence of Microbulbifer sp. YPW1 from mangrove sediments in Yanpu harbor, China.

Arch Microbiol 2021 Sep 28. Epub 2021 Sep 28.

Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China.

In this work, a strain named YPW1 was isolated from the sediments of an artificial mangrove in Yanpu harbor, China. A complete genome of YPW1 was sequenced and assembled. The 16S rRNA gene assigned strain YPW1 into genus Microbulbifer, and the maximum values of average nucleotide identity and digital DNA-DNA hybridization of ZHDP1 genome were 90. Read More

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September 2021

Chromosome-level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem.

Mol Ecol Resour 2021 Sep 28. Epub 2021 Sep 28.

State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.

Though the genomes of many rice herbivorous pests have recently been well characterized, little is known about the genome of their natural enemies. Here, by using the Illumina and PacBio platforms, we sequenced and assembled the whole genome of the mirid species Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), which is an economically and ecologically important natural enemy in the rice ecosystem acting as a dominant predator for planthoppers and leafhoppers in the field. Through Hi-C scaffolding, 1615 scaffolds with a total size of 338. Read More

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September 2021

Whole-Genome Sequencing of sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior.

Genes (Basel) 2021 Sep 15;12(9). Epub 2021 Sep 15.

Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.

sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. Read More

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September 2021

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease.

G3 (Bethesda) 2021 Sep;11(10)

Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.

Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce's disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1. Read More

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September 2021

De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus).

G3 (Bethesda) 2021 Sep;11(10)

Department of Biology, Brigham Young University, Provo, UT 84602, USA.

The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Read More

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September 2021

First complete chloroplast genome of the rare medicinal plant .

Mitochondrial DNA B Resour 2021 20;6(10):2993-2994. Epub 2021 Sep 20.

Chinese Herbal Medicine Industry Center of Xiushan Tujia and Miao Autonomous County, Chongqing, China.

is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of was sequenced and assembled based on the next generation sequencing. Read More

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September 2021

Genomic Resources to Guide Improvement of the Shea Tree.

Front Plant Sci 2021 9;12:720670. Epub 2021 Sep 9.

AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya.

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree () is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Read More

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September 2021

Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium subsp. .

Front Microbiol 2021 7;12:731711. Epub 2021 Sep 7.

Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan.

Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium subsp. . Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Read More

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September 2021

Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

Microb Genom 2021 Sep;7(9)

National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada.

Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. Read More

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September 2021

Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties.

Arch Microbiol 2021 Sep 22. Epub 2021 Sep 22.

Department of Microbiology and Fermentation Technology, CSIR Central Food Technological Research Institute, Mysuru, 570020, India.

Bifidobacterium longum NCIM 5672 is a probiotic strain isolated from the Indian infant feces. The probiotic efficacy of Bifidobacteria is majorly affected by its acid tolerance. This study determined the probiotic properties and acid-tolerance mechanism of B. Read More

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September 2021

The complete chloroplast genome sequence of a medicinal plant and phylogenetic analysis.

Authors:
Huixing Li

Mitochondrial DNA B Resour 2021 15;6(10):2957-2959. Epub 2021 Sep 15.

Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, Henan, China.

is a common ornamental arbor in the genus (family Rosaceae), which complete chloroplast (cp) genome was sequenced, assembled and annotated. The chloroplast genome of was 160,184 bp in length, including a large single copy (LSC) region of 88,121, a small single copy (SSC) region of 19,295 bp, and two inverted repeat (IR) regions of 26,384 bp. The GC contents of LSC, SSC, IR and whole genome are 36. Read More

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September 2021

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences.

BMC Plant Biol 2021 Sep 22;21(1):431. Epub 2021 Sep 22.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 100193, Beijing, People's Republic of China.

Background: Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L. Read More

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September 2021

A Draft Genome Assembly for the Eastern Fox Squirrel, Sciurus niger.

G3 (Bethesda) 2021 Sep 22. Epub 2021 Sep 22.

Virginia Museum of Natural History, 21 Starling Avenue, Martinsville, Virginia 24112, USA. 276.634.4177.

The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2. Read More

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September 2021

A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant.

Hortic Res 2020 Sep 21;7(1):153. Epub 2020 Sep 21.

Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021, China.

Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. Read More

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September 2020

VPsero: Rapid Serotyping of Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data.

Front Microbiol 2021 2;12:620224. Epub 2021 Sep 2.

BGI-Shenzhen, Shenzhen, China.

has emerged as a significant enteropathogen in human and marine habitats worldwide, notably in regions where aquaculture products constitute a major nutritional source. It is a growing cause of diseases including gastroenteritis, wound infections, and septicemia. Serotyping assays use commercially available antisera to identify strains, but this approach is limited by high costs, complicated procedures, cross-immunoreactivity, and often subjective interpretation. Read More

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September 2021

Improved Whole-Genome Sequence of Fusarium meridionale, the Fungal Pathogen Causing Fusarium Head Blight in Rice.

Mol Plant Microbe Interact 2021 Sep 17. Epub 2021 Sep 17.

Institute of Food Safey and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China;

Members of the Fusarium graminearum species complex (FGSC) cause extensive yield losses in cereal production worldwide and food safety concerns due to the accumulation of Fusarium toxins in infected grains. Among these pathogens, F. meridionale is responsible for Fusarium head blight of wheat and rice, ear and stalk rot of maize, and pod blight of soybean. Read More

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September 2021

Draft Genome Sequences of Fungi Isolated from the International Space Station during the Microbial Tracking-2 Experiment.

Microbiol Resour Announc 2021 Sep 16;10(37):e0075121. Epub 2021 Sep 16.

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA.

As part of the Microbial Tracking-2 study, 94 fungal strains were isolated from surfaces on the International Space Station, and whole-genome sequences were assembled. Characterization of these draft genomes will allow evaluation of microgravity adaption, risks to human health and spacecraft functioning, and biotechnological applications of fungi. Read More

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September 2021

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.

Cell Syst 2021 Sep 14. Epub 2021 Sep 14.

Department of Computational Biology, Institut Pasteur, Paris 75015, France. Electronic address:

DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of minimizer-space de Bruijn graphs to enable long-read genome assembly. mdBG achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without compromising accuracy. Read More

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September 2021

The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway.

Genomics 2021 Sep 11;113(6):3696-3704. Epub 2021 Sep 11.

State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518120, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Read More

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September 2021

Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000.

BMC Genomics 2021 Sep 13;22(1):655. Epub 2021 Sep 13.

CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India.

Background: Myxobacteria harbor numerous biosynthetic gene clusters that can produce a diverse range of secondary metabolites. Minicystis rosea DSM 24000 is a soil-dwelling myxobacterium belonging to the suborderSorangiineae and family Polyangiaceae and is known to produce various secondary metabolites as well as polyunsaturated fatty acids (PUFAs). Here, we use whole-genome sequencing to explore the diversity of biosynthetic gene clusters in M. Read More

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September 2021

Whole-genome sequencing and antimicrobial resistance analysis of multidrug-resistant Aeromonas veronii strain JC529 from a common carp.

J Glob Antimicrob Resist 2021 Sep 8;27:118-122. Epub 2021 Sep 8.

Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China. Electronic address:

Objectives: Aeromonas veronii can cause infections in humans and a wide variety of aquatic and terrestrial animals as well as causing serious economic losses in aquaculture worldwide. Aeromonas veronii strain JC529 was isolated from an infected common carp in a fish pond in Jilin Province. In this study, we identified the multidrug resistance genes and traced the source of the strain in order to lay the foundation for research on the resistance mechanisms of other Aeromonas isolates. Read More

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September 2021