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GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies [article]

Tomas Vetrovsky, Daniel Morais, Petr Kohout, Clementine Lepinay, Camelia Algora Gallardo, Sandra Awokunle Holla, Barbara Doreen Bahnmann, Kveta Bilohneda, Vendula Brabcova, Federica D'Alo, Zander Rainier Human, Mayuko Jomura (+21 others)
2020 bioRxiv   pre-print
The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it.  ...  To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats  ...  All corresponding authors of published studies that provided additional information on the samples included in the database are gratefully acknowledged.  ... 
doi:10.1101/2020.04.24.060384 fatcat:xg2234ejdvdcjhbdw53rueuszm

Streamlined Conversion of Omics Metadata into Manuscript Facilitates Publishing and Reuse of Omics Data

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
2020 Biodiversity Information Science and Standards  
The workflow streamlines automatic conversion and import of metadata from the European Nucleotide Archive (ENA) into an omics data paper manuscript created in the ARPHA Writing Tool (AWT), following a  ...  three step procedure: mapping of the European Nucleotide Archive (ENA) metadata to the manuscript sections, extraction of the relevant metadata through the ENA project or study ID, and transforming the  ...  This research has received partial funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764840.  ... 
doi:10.3897/biss.4.59041 fatcat:nfef2u26eng2tpj4suij3u3hjy

nData on genome resequencing of pigmented and non-pigmented Malaysian rice varieties

Rabiatul-Adawiah Zainal-Abidin, Zamri Zainal, Zeti-Azura Mohamed-Hussein, Yun Shin Sew, Sanimah Simoh, Shahril Firdaus Ab Razak, Norliza Abu-Bakar
2020 Data in Brief  
Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.  ...  The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits.  ...  Conflicts of Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.  ... 
doi:10.1016/j.dib.2020.105806 pmid:32566707 pmcid:PMC7298397 fatcat:cwfk7zreqrdkdkkkvpm4xhot7q

Complete Genome Sequence of a Bovine Ephemeral Fever Virus Isolate from Israel

Daniel L. W. Dorey-Robinson, Mar Fernández de Marco, Luis M. Hernández-Triana, Arran J. Folly, Lorraine M. McElhinney, Jessica E. Stokes, Chris Sanders, Simon Carpenter, Anthony R. Fooks, Olga Zalesky, Boris Gelman, Oran Erster (+2 others)
2019 Microbiology Resource Announcements  
Here, we report the first complete genome of a bovine ephemeral fever virus (BEFV) isolate from an infected bovine in Israel.  ...  The genome shares 95.3% identity with a Turkish genomic sequence but contains α3 and γ open reading frames that are truncated compared to those of existing BEFV genome sequences.  ...  ACKNOWLEDGMENTS This study was funded by grant SE4113 from the Department for Environment, Food and Rural Affairs (Defra), by the Scottish and Welsh governments, and by the European Union's Horizon 2020  ... 
doi:10.1128/mra.00822-19 pmid:31601661 pmcid:PMC6787318 fatcat:sd4uovy3hzdapgj7uibnxxdghe

Complete Genome Sequence of Bartonella alsatica Strain IBS 382 (CIP 105477)

Arno Thibau, Tilman G. Schultze, Wibke Ballhorn, Volkhard A. J. Kempf, J. Cameron Thrash
2020 Microbiology Resource Announcements  
Bartonella alsatica causes bacteremia in rabbits and, rarely, human infections.  ...  The availability of this genome sequence allows future work on understanding the zoonotic potential of this pathogen.  ...  ACKNOWLEDGMENTS This research was supported by the Viral and Bacterial Adhesin Network Training (ViBrANT) Program funded by the European Union HORIZON 2020 Research and Innovation Program under Marie Skłodowska-Curie  ... 
doi:10.1128/mra.00769-20 pmid:32816983 fatcat:wmv6mzazbze2vmxrc6mgzjvmje

DDBJ Database updates and computational infrastructure enhancement

2019 Nucleic Acids Research  
Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute.  ...  The Bioinformation and DDBJ Center ( in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Naofumi Ishikawa and all members of Bioinformation and DDBJ Center for their assistance in data collection, annotation, release  ... 
doi:10.1093/nar/gkz982 pmid:31724722 pmcid:PMC7145692 fatcat:uubxnpbeqvabrkkaw5ah4q7hzm

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'Anna, Dilmurat Yusuf, Björn Grüning, Rolf Backofen, Frederik Coppens
2021 Bioinformatics  
The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA.  ...  A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment.  ...  In the COVID-19 Data Portal (, the repository for SARS-CoV-2 nucleotide sequence data is the European Nucleotide Archive (ENA).  ... 
doi:10.1093/bioinformatics/btab421 pmid:34096994 fatcat:ube7ho4gs5baloejmvbykk4cee

The European Nucleotide Archive in 2019

2019 Nucleic Acids Research  
The European Nucleotide Archive (ENA, at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and  ...  access services across the spectrum of nucleotide sequence data types.  ...  have led to a broad range of nucleotide sequences that build the content of today's European Nucleotide Archive (ENA).  ... 
doi:10.1093/nar/gkz1063 pmid:31722421 pmcid:PMC7145635 fatcat:aorxf6izbvbkhb7jwbjawugaci

EarlyCause - Deliverable 2.1: Data Management Plan version 1

Jeena Rajan, Guy Cochrane
2020 Zenodo  
This deliverable addresses the purpose and description of data generated as part of the EarlyCause project and is comprised of a model for data handling during and after the project, including provision  ...  The project aims to make relevant data available for reusability by the community through public and specialised data repositories.  ...  European Nucleotide Archive (ENA) 2 , an ELIXIR Core Data Resource 3 , for full open data access.  ... 
doi:10.5281/zenodo.3961483 fatcat:pffzaujzizbsjcvhzshfv4hpfe

Complete Coding Sequences of Two Dengue Virus Type 2 Strains Isolated from an Outbreak in Burkina Faso in 2016

Cécile Baronti, Géraldine Piorkowski, Franck Touret, Rémi Charrel, Xavier de Lamballerie, Antoine Nougairede
2017 Genome Announcements  
We report here the complete coding sequences of two strains of dengue virus type 2, isolated in France from patients returning from Burkina Faso in November 2016.  ...  Both strains (cosmopolitan genotype) are almost identical (99.91% nucleotide identity) and closely related to a strain circulating in Burkina Faso in 1983.  ...  This work was supported by the European Virus Archive goes Global project (EVAg; European Union-Horizon 2020 program under grant agreement no. 653316.  ... 
doi:10.1128/genomea.00209-17 pmid:28450505 pmcid:PMC5408103 fatcat:x6dkzq5g25awnoz4i4pxdhqgte

OUP accepted manuscript

2017 Nucleic Acids Research  
In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content.  ...  Since 1987, the DNA Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community.  ...  The collaboration consists of three nodes: DNA Data Bank of Japan (DDBJ: http://www.ddbj. in Mishima, Japan (2); European Nucleotide Archive (ENA: in Hinxton, UK  ... 
doi:10.1093/nar/gkx1097 pmid:29190397 pmcid:PMC5753279 fatcat:aujil64o3zbkvpfa233kpi5pva

On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa

Mark Wong, Rhodri Leng
2020 F1000Research  
First, we retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each species.  ...  , countries of institution, year of first submission to the ENA, and the year of article publication, and 2) A .csv file documenting all institutions submitting to the ENA, number of nucleotides sequenced  ...  The staff at the Edinburgh DataShare repository provided assistance and service in uploading and indexing our datasets.  ... 
doi:10.12688/f1000research.18656.2 fatcat:kczeptjhk5f6bb37kpawx5ojm4

Genome Sequence of a Persistent Campylobacter jejuni Strain, 2016-IZSVE-19-111250

Arianna Peruzzo, Barbara Salerno, Alessia Tiengo, Sara Petrin, Lisa Barco, Carmen Losasso, Massimiliano Orsini, Steven R. Gill
2020 Microbiology Resource Announcements  
In this report, we present the whole-genome sequence of a Campylobacter jejuni strain isolated recursively for the last 3 years from an Italian poultry farm.  ...  The complete genome has been deposited in the NCBI assembly database with accession no. CP053659.1. The raw reads were uploaded to the European Nucleotide Archive database under the accession no.  ...  on November 16, 2020 by guest Downloaded from  ... 
doi:10.1128/mra.01033-20 pmid:33033140 fatcat:gopv6bkh7jb2now3uw7tdbi73u

Genome Sequence of Fusarium graminearum Strain CML3066, Isolated from a Wheat Spike in Southern Brazil

Ana K. Machado Wood, Robert King, Martin Urban, Camila P. Nicolli, Emerson M. Del Ponte, Kim E. Hammond-Kosack, Antonis Rokas
2020 Microbiology Resource Announcements  
We report here the annotated genome of a deoxynivalenol/15-acetyl-deoxynivalenol-producing Brazilian strain called CML3066, isolated from FHB-symptomatic wheat spikes collected in 2009.  ...  We thank Ludwig Pfenning for depositing the strain in the Coleção Micológica de Lavras (CML) in Brazil. We also thank the staff at the European Nucleotide Archive (ENA), Cambridge, United Kingdom.  ...  ACKNOWLEDGMENTS This research was supported by the Biotechnology and Biological Sciences Research Council of the United Kingdom (BBSRC) through the Institute Strategic Programmes 20:20 Wheat (BB/J/00426X  ... 
doi:10.1128/mra.00157-20 pmid:32381606 pmcid:PMC7206484 fatcat:yvzpr5b7erehvcrcb4q6wrjw2e

Nobel Prize 2020 in Chemistry honors CRISPR: a tool for rewriting the code of life

Lukas Westermann, Björn Neubauer, Michael Köttgen
2020 Pflügers Archiv: European Journal of Physiology  
The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material.  ...  If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly  ...  Emmanuelle Charpentier and Jennifer Doudna have been awarded the 2020 Nobel Prize in Chemistry for their work on CRISPR-Cas9-a method to edit DNA.  ... 
doi:10.1007/s00424-020-02497-9 pmid:33244639 pmcid:PMC7782372 fatcat:eycrrmg6g5djlmwku4xzvwug6u
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