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Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Ewers, Isabelle; Rajter, Lubomír; Czech, Lucas; Mahé, Frédéric; Stamatakis, Alexandros ORCID iD icon 1; Dunthorn, Micah
1 Institut für Theoretische Informatik (ITI), Karlsruher Institut für Technologie (KIT)

Abstract:

Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. ... mehr


Verlagsausgabe §
DOI: 10.5445/IR/1000161782
Veröffentlicht am 29.08.2023
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsmonat/-jahr 09.2023
Sprache Englisch
Identifikator ISSN: 1066-5234, 1550-7408
KITopen-ID: 1000161782
Erschienen in Journal of Eukaryotic Microbiology
Verlag John Wiley and Sons
Band 70
Heft 5
Seiten Art.Nr.: e12990
Vorab online veröffentlicht am 13.07.2023
Schlagwörter ciliates, diversity, environmental sequencing, phylogenetics, taxonomy
Nachgewiesen in Dimensions
Web of Science
Scopus
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