Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providin...

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Autores principales:	Ľubomír Rajter, Micah Dunthorn
Formato:	article
Lenguaje:	EN
Publicado:	Pensoft Publishers 2021
Materias:	Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/19d05a992dc541eeb7a0572256e4d1f3
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spelling	oai:doaj.org-article:19d05a992dc541eeb7a0572256e4d1f32021-12-02T18:53:39ZCiliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data10.3897/mbmg.5.696022534-9708https://doaj.org/article/19d05a992dc541eeb7a0572256e4d1f32021-08-01T00:00:00Zhttps://mbmg.pensoft.net/article/69602/download/pdf/https://mbmg.pensoft.net/article/69602/download/xml/https://mbmg.pensoft.net/article/69602/https://doaj.org/toc/2534-9708Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.Ľubomír RajterMicah DunthornPensoft PublishersarticleEcologyQH540-549.5ENMetabarcoding and Metagenomics, Vol 5, Iss , Pp 121-132 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ecology QH540-549.5
spellingShingle	Ecology QH540-549.5 Ľubomír Rajter Micah Dunthorn Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
description	Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.
format	article
author	Ľubomír Rajter Micah Dunthorn
author_facet	Ľubomír Rajter Micah Dunthorn
author_sort	Ľubomír Rajter
title	Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
title_short	Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
title_full	Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
title_fullStr	Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
title_full_unstemmed	Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
title_sort	ciliate ssu-rdna reference alignments and trees for phylogenetic placements of metabarcoding data
publisher	Pensoft Publishers
publishDate	2021
url	https://doaj.org/article/19d05a992dc541eeb7a0572256e4d1f3
work_keys_str_mv	AT lubomirrajter ciliatessurdnareferencealignmentsandtreesforphylogeneticplacementsofmetabarcodingdata AT micahdunthorn ciliatessurdnareferencealignmentsandtreesforphylogeneticplacementsofmetabarcodingdata
_version_	1718377312140918784

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

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