scholarly journals The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation

2019 ◽  
Vol 69 (4) ◽  
pp. 895-898 ◽  
Author(s):  
Linhuan Wu ◽  
Juncai Ma
Keyword(s):  
Genome Sequencing ◽  
Data Center ◽  
Type Strain ◽  
World Federation ◽  
Whole Genome ◽  
Culture Collections ◽  
Sequencing Project ◽  
The World ◽  
Type Strains ◽  
Evolutionary Microbiology

The World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology and contribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the wdcm and participant culture collections to submit a type strain sequencing proposal.

scholarly journals Skerman and beyond: 2019 status of the Global Catalogue of Microorganisms

2019 ◽  
Vol 40 (3) ◽  
pp. 121
Author(s):  
Juncai Ma ◽  
Linhuan Wu ◽  
İpek Kurtböke
Keyword(s):  
Type Strain ◽  
Reference Strain ◽  
World Federation ◽  
Culture Collections ◽  
Late Professor ◽  
Sequencing Project ◽  
Data Centre ◽  
The World ◽  
The Status ◽  
Set Up

The World Federation for Culture Collections (WFCC)-MIRCEN World Data Centre for Microorganisms (WDCM) was set up as a data centre of WFCC and UNESCO World Network of Microbiological Resources Centres (MIRCEN). The WDCM is a vehicle for networking microbial resource centres of various types of microorganisms. It also serves as an information resource for the customers of the microbial resource centres (http://www.wdcm.org/). The WDCM was established in 1966 by the late Professor V.B.D. Skerman in Australia, later moved to Japan in 1986 and since 2010 is based in China under the Directorship of Dr Juncai Ma. Current databases at the WDCM are the Culture Collections Information Worldwide (CCINFO), Global Catalogue of Microorganisms (GCM) and the WDCM Reference Strain Catalogue. In addition, Analyzer of Bio-resource citations (ABC) and Statistics on Patented Microorganisms are available (http://www.wdcm.org/databases.html). In this article the status of the GCM and its associated 10K type strain sequencing project that currently provides services to taxonomists for standard genome sequencing and annotation will be communicated.

scholarly journals Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Kevin Cole ◽  
Dona Foster ◽  
Julie E. Russell ◽  
Tanya Golubchik ◽  
Martin Llewelyn ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Accurate Identification ◽  
Access To Data ◽  
Type Strains

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.

scholarly journals Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Daniel Jaén-Luchoro ◽  
Carolina Seguí ◽  
Francisco Aliaga-Lozano ◽  
Francisco Salvà-Serra ◽  
Antonio Busquets ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Nontuberculous Mycobacterium ◽  
Whole Genome ◽  
Type Strains

Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains.

scholarly journals Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
David Smith ◽  
Matthew Ryan
Keyword(s):  
Best Practice ◽  
New Technologies ◽  
World Federation ◽  
Full Potential ◽  
Management Options ◽  
Culture Collections ◽  
Biological Resources ◽  
Preservation Method ◽  
The World ◽  
The Uk

Authentic, well preserved living organisms are basic elements for research in the life sciences and biotechnology. They are grown and utilized in laboratories around the world and are key to many research programmes, industrial processes and training courses. They are vouchers for publications and must be available for confirmation of results, further study or reinvestigation when new technologies become available. These biological resources must be maintained without change in biological resource collections. In order to achieve best practice in the maintenance and provision of biological materials for industry, research and education the appropriate standards must be followed. Cryopreservation is often the best preservation method available to achieve these aims, allowing long term, stable storage of important microorganisms. To promulgate best practice the Organisation for Economic Development and Co-operation (OECD published the best practice guidelines for BRCs. The OECD best practice consolidated the efforts of the UK National Culture Collections, the European Common Access to Biological Resources and Information (CABRI) project consortium and the World Federation for Culture Collections. The paper discusses quality management options and reviews cryopreservation of fungi, describing how the reproducibility and quality of the technique is maintained in order to retain the full potential of fungi.

scholarly journals Exploring the Diversity of Bacillus whole genome sequencing projects using Peasant, the Prokaryotic Assembly and Annotation Tool

2017 ◽  
Author(s):  
Jonathon Brenner ◽  
Laurynas Kalesinskas ◽  
Catherine Putonti
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Annotation Tool ◽  
Illumina Platform ◽  
Desktop Computer ◽  
High Quality ◽  
Sequencing Project ◽  
Computational Resources

ABSTRACTBackgroundThe persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects.ResultsThe Prokaryotic Assembly and Annotation Tool, Peasant, automates the processes of read quality control, genome assembly, and annotation for microbial sequencing projects. High-quality assemblies and annotations can be generated by Peasant without the need of programming expertise or high-performance computing resources. Furthermore, statistics are calculated so that users can evaluate their sequencing project. To illustrate the computational speed and accuracy of Peasant, the SRA records of 322 Illumina platform whole genome sequencing assays for Bacillus species were retrieved from NCBI, assembled and annotated on a single desktop computer. From the assemblies and annotations produced, a comprehensive analysis of the diversity of over 200 high-quality samples was conducted, looking at both the 16S rRNA phylogenetic marker as well as the Bacillus core genome.ConclusionsPeasant provides an intuitive solution for high-quality whole genome sequence assembly and annotation for users with limited programing experience and/or computational resources. The analysis of the Bacillus whole genome sequencing projects exemplifies the utility of this tool. Furthermore, the study conducted here provides insight into the diversity of the species, the largest such comparison conducted to date.

scholarly journals The Emergence and Spread of Novel SARS-CoV-2 Variants

2021 ◽  
Vol 9 ◽  
Author(s):  
Huaimin Yi ◽  
Jin Wang ◽  
Jiong Wang ◽  
Yuying Lu ◽  
Yali Zhang ◽  
...  
Keyword(s):  
Immune Response ◽  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neutralizing Antibodies ◽  
Whole Genome ◽  
Distribution Characteristics ◽  
S Protein ◽  
The World ◽  
Viral Genes

Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.

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