EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F18%3A00497733" target="_blank" >RIV/60077344:_____/18:00497733 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1371/journal.pbio.2005849" target="_blank" >https://doi.org/10.1371/journal.pbio.2005849</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pbio.2005849" target="_blank" >10.1371/journal.pbio.2005849</a>

Result language

angličtina

Original language name

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Original language description

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA Data-Bank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/EF16_019%2F0000759" target="_blank" >EF16_019/0000759: Centre for research of pathogenicity and virulence of parasites</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

PLoS Biology

ISSN

1545-7885

e-ISSN

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Volume of the periodical

16

Issue of the periodical within the volume

9

Country of publishing house

US - UNITED STATES

Number of pages

14

Pages from-to

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UT code for WoS article

000446154800012

EID of the result in the Scopus database

2-s2.0-85054785575