Colpodean ciliate phylogeny and reference alignments for phylogenetic placements

Rajter, Ľubomír; Ewers, Isabelle; Graupner, Nadine; Vďačný, Peter; Dunthorn, Micah

doi:10.1016/j.ejop.2020.125747

Cited by 5 publications

(22 citation statements)

References 41 publications

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“…These programs require a reference alignment and a reference tree. In ciliates, there is a recent reference alignment and tree for just the colpodean ciliates (Rajter et al 2021) but recent global reference alignments and trees for all ciliates are lacking.…”

Section: Introductionmentioning

confidence: 99%

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

Rajter¹,

Dunthorn²

2021

MBMG

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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.

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Section: Introductionmentioning

confidence: 99%

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

Rajter¹,

Dunthorn²

2021

MBMG

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“…In previous work, and in our study, B . pulchra was always the earliest divergent branch of Colpodida in the SSU‐rRNA gene tree, which means it has been stable between Colpodida and Cyrtolophosidida (Bourland et al, 2011 ; Dunthorn et al, 2012 ; Rajter et al, 2020 ; Vďačný & Foissner, 2019 ). But, we established multiple gene trees and they all confirmed the instability of the position of B .…”

Section: Discussionmentioning

confidence: 99%

“…Four major Colpodea lineages (Bursariomorphida, Platyophryida, Cyrtolophosidida, and Colpodida) have been identified by phylogenetic inference based on nuclear small subunit ribosomal RNA (nSSU‐rRNA) sequences (Dunthorn et al, 2008 ; Foissner et al, 2011 ; Vďačný & Foissner, 2019 ). Among these, Bursariomorphida (Fernández‐Galiano, 1979 ) was found to include in the taxa previously assigned to the order Bryometopida (Foissner, 1985 ; Vďačný & Foissner, 2019 ); the position of Platyophryida is indeterminate (Bourland et al, 2011 ; Rajter et al, 2020 ), Cyrtolophosidida is divided into two main clades, and Colpodida is the most complex clade (Foissner et al, 2011 ). Dunthorn et al ( 2014 ) investigated Colpodea phylogeny based on mtSSU‐rRNA gene sequence data and reported the same four lineages as those from the nSSU‐rRNA analyses mentioned earlier.…”

Section: Introductionmentioning

confidence: 99%

“…Dunthorn et al ( 2014 ) investigated Colpodea phylogeny based on mtSSU‐rRNA gene sequence data and reported the same four lineages as those from the nSSU‐rRNA analyses mentioned earlier. Nevertheless, there are inconsistencies in the evolutionary relationships among taxa within Colpodea (e.g., the position of Platyophryida), indicating that phylogenetic analysis based on a single gene is problematic (Rajter et al, 2020 ). Furthermore, species sampling remains unbalanced in Clopodea (e.g., there is only one species in Ilsiellidae and Bardeliellidae) that has led to the formation of paraphyletic groups and uncertainty in the assignment of various taxa (Fan et al, 2013 ; Foissner & Stoeck, 2009 ; Quintela‐Alonso et al, 2011 ; Strüder‐Kypke et al, 2000 ; Vďačný & Foissner, 2019 ; Zhao et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Song

Hao

et al. 2022

Ecology and Evolution

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In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU-rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two-gene concatenated dataset. For the first time, multi-genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and mtSSU-rRNA gene sequences of C. reniformis and C. grandis are provided for the first time, and these two species group into the clade including C. inflata, C. lucida, C. cucullus, and C. henneguyi; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be 'Hausmanniellidae with sharply shortened and isometric leftmost 1-4 ciliary rows' and Colpoda elliotti is transferred to Emarginatophrya; (4) the genus Colpoda is still non-monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C. inflata, C. lucida, C. cucullus, C. henneguyi, C. reniformis, and C. grandis, Group II comprises C. maupasi and C. ecaudata, and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups;(5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P. steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae.

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“…Ideally, to avoid duplicating work, to ensure high quality, and to provide stable points of reference for comparison between studies, suitable reference trees should be provided by the respective research/organismal communities. First efforts for microbial eukaryotes are on their way ( Berney et al, 2017 ; Del Campo et al, 2018 ; Rajter and Dunthorn, 2021 ; Rajter et al, 2021 ), although some of these are not designed explicitly for phylogenetic placements, but more taxonomic groups will follow. Recently, efforts have also been made to produce reference trees for higher order animals, such as fish ( Collins et al, 2021 ).…”

Section: Phylogenetic Placementmentioning

confidence: 99%

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

et al. 2022

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Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.

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Colpodean ciliate phylogeny and reference alignments for phylogenetic placements

Cited by 5 publications

References 41 publications

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

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

Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

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