55 results match your criteria platform k-mer


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

First report of bean common mosaic virus infecting heavenly bamboo (Nandina domestica) in China.

Plant Dis 2021 Sep 21. Epub 2021 Sep 21.

Zhejiang A and F University, 12627, College of Forestry and Biotechnology, Hangzhou, Zhejiang, China;

Heavenly bamboo (Nandina domestica) is an evergreen ornamental plant with worldwide distribution. In May 2018, seven out of twenty N. domestica plants showing virus-like symptoms, such as yellow mosaic and curling, were observed in Lin'an, Zhejiang province. Read More

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September 2021

KARGA: Multi-platform Toolkit for -mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data.

IEEE EMBS Int Conf Biomed Health Inform 2021 Jul 10;2021. Epub 2021 Aug 10.

Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA.

High-throughput sequencing is widely used for strain detection and characterization of antibiotic resistance in microbial metagenomic samples. Current analytical tools use curated antibiotic resistance gene (ARG) databases to classify individual sequencing reads or assembled contigs. However, identifying ARGs from raw read data can be time consuming (especially if assembly or alignment is required) and challenging, due to genome rearrangements and mutations. Read More

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Harmonization of whole-genome sequencing for outbreak surveillance of and .

Microb Genom 2021 Jul;7(7)

Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands.

Whole-genome sequencing (WGS) is becoming the de facto standard for bacterial typing and outbreak surveillance of resistant bacterial pathogens. However, interoperability for WGS of bacterial outbreaks is poorly understood. We hypothesized that harmonization of WGS for outbreak surveillance is achievable through the use of identical protocols for both data generation and data analysis. Read More

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Genome survey and microsatellite motif identification of Pogonophryne albipinna.

Biosci Rep 2021 Jul;41(7)

Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Read More

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Whole genome survey and microsatellite motif identification of Artemia franciscana.

Biosci Rep 2021 03;41(3)

Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.

Artemia is an industrially important genus used in aquaculture as a nutritious diet for fish and as an aquatic model organism for toxicity tests. However, despite the significance of Artemia, genomic research remains incomplete and knowledge on its genomic characteristics is insufficient. In particular, Artemia franciscana of North America has been widely used in fisheries of other continents, resulting in invasion of native species. Read More

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Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing.

BMC Res Notes 2021 Feb 2;14(1):42. Epub 2021 Feb 2.

Institute Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.

Objective: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. Read More

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February 2021

Clover: a clustering-oriented de novo assembler for Illumina sequences.

BMC Bioinformatics 2020 Nov 17;21(1):528. Epub 2020 Nov 17.

Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.

Background: Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. Read More

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November 2020

ARDEP, a Rapid Degenerate Primer Design Pipeline Based on -mers for Amplicon Microbiome Studies.

Int J Environ Res Public Health 2020 08 17;17(16). Epub 2020 Aug 17.

Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.

The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). Read More

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Genome survey of Chinese fir (Cunninghamia lanceolata): Identification of genomic SSRs and demonstration of their utility in genetic diversity analysis.

Sci Rep 2020 03 13;10(1):4698. Epub 2020 Mar 13.

The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A & F University, Lin'an, Hangzhou, 311300, Zhejiang, China.

Chinese fir (Cunninghamia lanceolata) is an important coniferous species that accounts for 20-30% of the total commercial timber production in China. Though traditional breeding of Chinese fir has achieved remarkable success, molecular-assisted breeding has made little progress due to limited availability of genomic information. In this study, a survey of Chinese fir genome was performed using the Illumina HiSeq Xten sequencing platform. Read More

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Whole-genome sequencing and analysis of the Chinese herbal plant .

Acta Pharm Sin B 2020 Feb 16;10(2):374-382. Epub 2019 Aug 16.

Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China.

Background: () (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family.

Method: Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used.

Results: A total of 56. Read More

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February 2020

A computational platform to identify origins of replication sites in eukaryotes.

Brief Bioinform 2021 03;22(2):1940-1950

Center for Informational Biology at University of Electronic Science and Technology of China.

The locations of the initiation of genomic DNA replication are defined as origins of replication sites (ORIs), which regulate the onset of DNA replication and play significant roles in the DNA replication process. The study of ORIs is essential for understanding the cell-division cycle and gene expression regulation. Accurate identification of ORIs will provide important clues for DNA replication research and drug development by developing computational methods. Read More

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High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish ().

G3 (Bethesda) 2020 03 5;10(3):877-880. Epub 2020 Mar 5.

Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding,

The big-eye mandarin fish () is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of would provide a foundation for better examining its genetic diversity and population history. Read More

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[Genome survey and characteristic analysis of SSR in Callicarpa nudiflora].

Zhongguo Zhong Yao Za Zhi 2019 Sep;44(18):3974-3978

College of Horticulture,Hainan University Haikou 570228,China.

Callicarpa nudiflora,which is a big brand of Li nationality medicine with Hainan characteristics,has the effects of dissolving stasis,hemostasis,anti-inflammatory and antibacterial. At present,there is a lack of information about the reference genome of C. nudiflora. Read More

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September 2019

A chromosomal-level genome assembly for the giant African snail Achatina fulica.

Gigascience 2019 10;8(10)

National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.

Background: Achatina fulica, the giant African snail, is the largest terrestrial mollusk species. Owing to its voracious appetite, wide environmental adaptability, high growth rate, and reproductive capacity, it has become an invasive species across the world, mainly in Southeast Asia, Japan, the western Pacific islands, and China. This pest can damage agricultural crops and is an intermediate host of many parasites that can threaten human health. Read More

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October 2019

CORAL: Verification-Aware OpenCL Based Read Mapper for Heterogeneous Systems.

IEEE/ACM Trans Comput Biol Bioinform 2021 Jul-Aug;18(4):1426-1438. Epub 2021 Aug 6.

Genomics has the potential to transform medicine from reactive to a personalized, predictive, preventive, and participatory (P4) form. Being a Big Data application with continuously increasing rate of data production, the computational costs of genomics have become a daunting challenge. Most modern computing systems are heterogeneous consisting of various combinations of computing resources, such as CPUs, GPUs, and FPGAs. Read More

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The evolution study on by whole-genome sequencing.

J Genet 2019 Sep;98

Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, People's Republic of China.

The species of was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100. Read More

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September 2019

Diagnostic Optical Sequencing.

ACS Appl Mater Interfaces 2019 Oct 20;11(39):35587-35596. Epub 2019 Sep 20.

Advances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multiomics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances toward such diagnostics. However, the inability to squeeze light with several hundred nanometer wavelengths into angstrom-scale volume for single-nucleotide measurements has hindered further progress. Read More

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October 2019

Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data.

Front Microbiol 2019 7;10:1683. Epub 2019 Aug 7.

C&K Genomics, Songpa-gu, South Korea.

Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA sequence analysis. However, the high cost of operation, difficulty in distinguishing between similar species, and limitations of the current sequencing technologies have made it difficult to obtain accurate results using these tools. Read More

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Genome Sequence Assembly of Dwarf Coconut ( L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species.

G3 (Bethesda) 2019 08 8;9(8):2377-2393. Epub 2019 Aug 8.

Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031

We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. Read More

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Identification and differential expression of piRNAs in the gonads of Amur sturgeon ().

PeerJ 2019 12;7:e6709. Epub 2019 Apr 12.

Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China.

Objective: Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. Read More

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De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis.

DNA Res 2019 Jun;26(3):195-203

Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. Read More

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Fast and flexible bacterial genomic epidemiology with PopPUNK.

Genome Res 2019 02 24;29(2):304-316. Epub 2019 Jan 24.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.

The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (ulation artitioning sing ucleotide -mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Read More

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February 2019

Genome survey on invasive veined rapa whelk () and development of microsatellite loci on large scale.

J Genet 2018 Aug 11;97(4):e79-e86. Epub 2018 Aug 11.

CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong, People's Republic of China.

The veined rapa whelk () is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. Read More

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A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes.

Gigascience 2018 09 1;7(9). Epub 2018 Sep 1.

CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China.

Background: Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family. Read More

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September 2018

Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub.

Gigascience 2018 07;7(7)

College of Life and Evironmental Sciences, Minzu University of China, 27 Zhongguancun South Street, Beijing, 100081, China.

Background: Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. Read More

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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

mSystems 2018 May-Jun;3(3). Epub 2018 Apr 10.

School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Read More

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Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly.

Gigascience 2018 03;7(3):1-6

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia.

Background: Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Read More

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Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome.

Gigascience 2017 12;6(12):1-7

Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China.

Background: Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Read More

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December 2017

Draft genome of the reindeer (Rangifer tarandus).

Gigascience 2017 12;6(12):1-5

Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China.

Background: The reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and it is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer, as well as males, regularly grow cranial appendages (antlers, the defining characteristics of cervids). Moreover, reindeer milk contains more protein and less lactose than bovids' milk. Read More

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December 2017