• Je něco špatně v tomto záznamu ?

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

J. Del Campo, M. Kolisko, V. Boscaro, LF. Santoferrara, S. Nenarokov, R. Massana, L. Guillou, A. Simpson, C. Berney, C. de Vargas, MW. Brown, PJ. Keeling, L. Wegener Parfrey,

. 2018 ; 16 (9) : e2005849. [pub] 20180917

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz   https://www.medvik.cz/link/bmc19028206

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 DataBank 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.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc19028206
003      
CZ-PrNML
005      
20190816111851.0
007      
ta
008      
190813s2018 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1371/journal.pbio.2005849 $2 doi
035    __
$a (PubMed)30222734
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Del Campo, Javier $u Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain. Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
245    10
$a EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution / $c J. Del Campo, M. Kolisko, V. Boscaro, LF. Santoferrara, S. Nenarokov, R. Massana, L. Guillou, A. Simpson, C. Berney, C. de Vargas, MW. Brown, PJ. Keeling, L. Wegener Parfrey,
520    9_
$a 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 DataBank 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.
650    _2
$a Ciliophora $x genetika $7 D016798
650    12
$a datové kurátorství $7 D066289
650    _2
$a databáze genetické $7 D030541
650    _2
$a Eukaryota $x klasifikace $x genetika $7 D056890
650    12
$a genetická variace $7 D014644
650    12
$a fylogeneze $7 D010802
650    _2
$a RNA ribozomální $x genetika $7 D012335
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
655    _2
$a Research Support, U.S. Gov't, Non-P.H.S. $7 D013486
700    1_
$a Kolisko, Martin $u Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada. Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
700    1_
$a Boscaro, Vittorio $u Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
700    1_
$a Santoferrara, Luciana F $u Departments of Marine Sciences & Ecology and Evolutionary Biology, University of Connecticut, Storrs, United States of America.
700    1_
$a Nenarokov, Serafim $u Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
700    1_
$a Massana, Ramon $u Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain.
700    1_
$a Guillou, Laure $u Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France.
700    1_
$a Simpson, Alastair $u Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.
700    1_
$a Berney, Cedric $u Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France.
700    1_
$a de Vargas, Colomban $u Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France.
700    1_
$a Brown, Matthew W $u Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America.
700    1_
$a Keeling, Patrick J $u Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
700    1_
$a Wegener Parfrey, Laura $u Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada. Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
773    0_
$w MED00008061 $t PLoS biology $x 1545-7885 $g Roč. 16, č. 9 (2018), s. e2005849
856    41
$u https://pubmed.ncbi.nlm.nih.gov/30222734 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20190813 $b ABA008
991    __
$a 20190816112121 $b ABA008
999    __
$a ok $b bmc $g 1433355 $s 1066666
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2018 $b 16 $c 9 $d e2005849 $e 20180917 $i 1545-7885 $m PLoS biology $n Plos Biol $x MED00008061
LZP    __
$a Pubmed-20190813
Zpět

Najít záznam

Citační ukazatele

Možnosti archivace