• Je něco špatně v tomto záznamu ?

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

AK. Tice, D. Žihala, T. Pánek, RE. Jones, ED. Salomaki, S. Nenarokov, F. Burki, M. Eliáš, L. Eme, AJ. Roger, A. Rokas, XX. Shen, JFH. Strassert, M. Kolísko, MW. Brown

. 2021 ; 19 (8) : e3001365. [pub] 20210806

Jazyk angličtina Země Spojené státy americké

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

Perzistentní odkaz   https://www.medvik.cz/link/bmc22003946

Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc22003946
003      
CZ-PrNML
005      
20220127145712.0
007      
ta
008      
220113s2021 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1371/journal.pbio.3001365 $2 doi
035    __
$a (PubMed)34358228
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Tice, Alexander K $u Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America $u Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
245    10
$a PhyloFisher: A phylogenomic package for resolving eukaryotic relationships / $c AK. Tice, D. Žihala, T. Pánek, RE. Jones, ED. Salomaki, S. Nenarokov, F. Burki, M. Eliáš, L. Eme, AJ. Roger, A. Rokas, XX. Shen, JFH. Strassert, M. Kolísko, MW. Brown
520    9_
$a Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.
650    _2
$a Eukaryota $x genetika $7 D056890
650    12
$a fylogeneze $7 D010802
650    12
$a software $7 D012984
655    _2
$a hodnotící studie $7 D023362
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 Žihala, David $u Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
700    1_
$a Pánek, Tomáš $u Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America $u Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
700    1_
$a Jones, Robert E $u Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America $u Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
700    1_
$a Salomaki, Eric D $u Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic
700    1_
$a Nenarokov, Serafim $u Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic
700    1_
$a Burki, Fabien $u Department of Organismal Biology, Uppsala University, Uppsala, Sweden $u Science for Life Laboratory, Uppsala University, Uppsala, Sweden
700    1_
$a Eliáš, Marek $u Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
700    1_
$a Eme, Laura $u Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Saclay, Paris, France
700    1_
$a Roger, Andrew J $u Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
700    1_
$a Rokas, Antonis $u Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
700    1_
$a Shen, Xing-Xing $u State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
700    1_
$a Strassert, Jürgen F H $u Department of Organismal Biology, Uppsala University, Uppsala, Sweden $u Leibniz Institute of Freshwater Ecology and Inland Fisheries, Ecosystem Research, Berlin, Germany
700    1_
$a Kolísko, Martin $u Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic $u Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
700    1_
$a Brown, Matthew W $u Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America $u Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
773    0_
$w MED00008061 $t PLoS biology $x 1545-7885 $g Roč. 19, č. 8 (2021), s. e3001365
856    41
$u https://pubmed.ncbi.nlm.nih.gov/34358228 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y p $z 0
990    __
$a 20220113 $b ABA008
991    __
$a 20220127145708 $b ABA008
999    __
$a ok $b bmc $g 1751416 $s 1155095
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2021 $b 19 $c 8 $d e3001365 $e 20210806 $i 1545-7885 $m PLoS biology $n Plos Biol $x MED00008061
LZP    __
$a Pubmed-20220113

Najít záznam

Citační ukazatele

    Možnosti archivace