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

Rajter, Ľubomír; Dunthorn, Micah

doi:10.3897/mbmg.5.69602

Cited by 6 publications

(10 citation statements)

References 74 publications

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“…Interestingly, the clade of Caenomorphidae resulted sister of Muranotrichea in our phylogenetic analyses, throughout low support, rather than to Litostomatea as in previous analyses (Li et al, 2017; Rotterová et al, 2020). The family Caenomorphidae is a clade of anaerobic ciliates with an uncertain position within Ciliophora (Rajter & Dunthorn, 2021).…”

Section: Discussionmentioning

confidence: 99%

Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora)

Méndez-Sánchez

Pomahač

Rotterová

et al. 2023

J Eukaryotic Microbiology

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The diversity of the classes Odontostomatea and Muranotrichea, which contain solely obligate anaerobes, is poorly understood. We studied two populations of Mylestoma sp., one of Saprodinium dentatum (Odontostomatea), two of Muranothrix felix sp. nov., and one of Muranothrix sp. (Muranotrichea) employing live observation, protargol impregnation, scanning electron microscopy, and 18S rRNA gene sequencing. Conspecificity of Mylestoma sp., described here, with a previously described species of this genus cannot be excluded since no species have been studied with modern methods. Phylogenetically, the genus Mylestoma is closely related to the odontostomatid Discomorphella pedroeneasi, although the phylogenetic position of class Odontostomatea itself remains unresolved. The newly described muranotrichean species, Muranothrix felix sp. nov., is morphologically similar to M. gubernata but can be distinguished by its fewer macronuclear nodules and fewer adoral membranelles; moreover, it is clearly distinguished from M. gubernata by its 18S rRNA gene sequence. Another population, designated here as Muranothrix sp., most likely represents a separate species.

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Section: Discussionmentioning

confidence: 99%

Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora)

Méndez-Sánchez

Pomahač

Rotterová

et al. 2023

J Eukaryotic Microbiology

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“…Consequently, we would highly encourage such collaborations, and the public sharing of (perhaps even versioned instances of) gold-standard reference trees. Notably, for some environments, first efforts into this direction have already been undertaken ( Berney et al, 2017 ; Del Campo et al, 2018 ; Rubinat-Ripoll, 2019 ; Rajter and Dunthorn, 2021 ; Rajter et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…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%

“…Generally, a number of RSs in the order of hundreds to a few thousands has shown to provide enough coverage for most QS datasets, while still being small enough to properly visualize their phylogeny and to conduct all necessary computations in reasonable time. Often, it is sufficient to include a single species to represent a whole clade ( Rajter and Dunthorn, 2021 ). Depending on the types of downstream analyses, it can be a disadvantage to select sequences that are too similar to each other (i. e., closely related species, or different strains of the same species), as this can spread the placement distribution across nearby branches.…”

Section: Phylogenetic Placementmentioning

confidence: 99%

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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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“…This limitation has brought to the development of tools that can increase the taxonomic resolution of HTS short reads (Matsen et al 2012 ; Gwak and Rho 2020 ). Among these, the phylogenetic placement is one of the most interesting and increasingly used approach (Rajter and Dunthorn 2021 ). It has been successfully applied to place the short reads on phylogenetic trees built using full-length reference sequences, allowing their assignment at species level (Matsen et al 2012 ; Janssen et al 2018 ), showing a greater accuracy than de novo (i.e., based only on short reads) tree construction (Balaban et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

Banchi

Manna

Fonti

et al. 2022

Environ Sci Pollut Res

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The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.

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

Cited by 6 publications

References 74 publications

Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora)

Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora)

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

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

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