Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)

Ganser, Maximilian H.; Santoferrara, Luciana F.

doi:10.1016/j.ympev.2022.107433

Cited by 7 publications

(6 citation statements)

References 110 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The consistency of the detected characters can be further evaluated by comparing their presence between the reference and alternative alignments ( https://github.com/maxganser/consistency‐script ). Here, we used the curated Oligotrichea reference alignment of 18S rRNA gene sequences provided by Ganser et al ( 2022 ) plus the sequence FJ480419 of Strombidium basimorphum (Zhang et al, 2010 ), setting the species S. biarmatum , S. basimorphum , and S. paracapitatum as query group and the remaining oligotrichids as reference group. Further marker gene sequences (e.g., 28S rRNA, ITS regions, or COI) are currently not available for all three species.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, both layers were generally lumped in the present study into an electron-dense layer surrounding an electrontransparent lumen. Ganser et al (2022) suggested the inclusion of molecular signatures as characters in the diagnoses of taxa that are morphologically distinct and provided clear guidelines for their detection and evaluation. We used the tool DeSignate through its web interface (Hütter et al, 2020; https://github.com/Datab aseGr oup/DeSig nate) to identify potential molecular signature characters which are specified by their position and discrete state (i.e., A, T, G, C, or a gap) in a reference alignment.…”

Section: Terminologymentioning

confidence: 99%

See 1 more Smart Citation

Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha)

Agatha,

Weißenbacher,

Kirschner

et al. 2023

J Eukaryotic Microbiology

Self Cite

View full text Add to dashboard Cite

Strombidium is a species‐rich genus of oligotrichid ciliates mainly inhabiting the marine pelagial. In molecular phylogenies, the genus emerged as non‐monophyletic, and cladistic analyses suggest that it is largely characterized by plesiomorphies. A reliable split of the genus and the establishment of new genera necessitate, however, support by novel morphological and/or ultrastructural features. In the present study, the arrangement and ultrastructure of trichites are proposed as taxonomically relevant characters. Strombidium biarmatum Agatha et al., 2005 differs in the trichite pattern from the type species Strombidium sulcatum and most congeners. Aside from the trichites inserting anteriorly to the girdle kinety and generating the typical funnel‐shaped complex in the posterior cell portion, the species displays additional trichites between the adoral membranelles even visible in live cells. Here, this exceptional trichite arrangement is detailed based on transmission electron microscopic investigations. In molecular phylogenies, S. biarmatum forms a monophylum with two congeners sharing its trichite arrangement. Therefore, the strombidiid genus Heteropilum nov. gen. is established with S. biarmatum as type species to also include H. paracapitatum (Song et al., 2015) nov. comb. and H. basimorphum (Martin & Montagnes, 1993) nov. comb. Further differences discovered in the trichite ultrastructure support the organelles' taxonomic significance.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Terminologymentioning

confidence: 99%

Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha)

Agatha,

Weißenbacher,

Kirschner

et al. 2023

J Eukaryotic Microbiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Identification was done with a naïve Bayes classifier (Bokulich et al, 2018) against the PR2 database v4.12.0 (Guillou et al, 2013) trimmed to contain only the V4 region. Taxonomic assignment was complemented with BLAST+ v2.12.0 (Camacho et al, 2009) and phylogenetic trees (built in the same way as described below in "Other phylogenetic analyses"), using the EukRef-Ciliophora curated dataset (Boscaro et al, 2018) and a curated alignment for Oligotrichea (Ganser et al, 2022). The complementation of three reference datasets was needed due to uneven curation of ciliate sequences in the PR2 version available at the time of analysis; all three references have now been reconciled and are available in PR2 v5.0.0 (Santoferrara and Ganser, in Vaulot, 2023).…”

Section: Sequence Processing Identification and Curation Of Ciliate S...mentioning

confidence: 99%

The photic‐aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean

Santoferrara

Qureshi

Sher

et al. 2023

J Eukaryotic Microbiology

Self Cite

View full text Add to dashboard Cite

The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi‐ and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny‐based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0–1000 m) at the Bermuda Atlantic Time‐series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha‐diversity (based on Faith's phylogenetic diversity index) from surface to 1000‐m waters. Second, multivariate analyses of beta‐diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade‐level correlations (EPA‐ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti‐correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha‐diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with the prevalence of algivory and mixotrophy vs. omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.

show abstract

“…This approach is useful in the case of eukaryotes, whose genomic reconstruction is limited compared to prokaryotes [ 16 ]. Among eukaryotes, distinctive molecular patterns are generally used to resolve the taxonomy of closely related species [ 17 ] or to analyze geographic patterns [ 18 ]. A recent study demonstrated the usefulness of DNA signatures to facilitate the taxonomic identification of ciliated protists [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

“…Among eukaryotes, distinctive molecular patterns are generally used to resolve the taxonomy of closely related species [ 17 ] or to analyze geographic patterns [ 18 ]. A recent study demonstrated the usefulness of DNA signatures to facilitate the taxonomic identification of ciliated protists [ 18 ]. Therefore, the nuclear and mitochondrial genes of a microbial eukaryote may bear the signatures needed to integrate both phylogenetic and ecological information.…”

Section: Introductionmentioning

confidence: 99%

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity

Barrenechea Angeles,

Nguyen,

Greco

et al. 2024

PLoS ONE

View full text Add to dashboard Cite

Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.

show abstract

Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)

Cited by 7 publications

References 110 publications

Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha)

Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha)

The photic‐aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity

Contact Info

Product

Resources

About