Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea)
Ciliated protists in the subclasses Choreotrichia and Oligotrichia are major components of marine plankton. Despite their ecological relevance, there are uncertainties in their systematics and diversity. We retrieved and curated all the GenBank ribosomal DNA (rDNA) sequences from these groups, which...
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todo:paper_10557903_v112_n_p12_Santoferrara2023-10-03T16:00:48Z Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) Santoferrara, L.F. Alder, V.V. McManus, G.B. Ciliate Environmental sequencing Protist Sequence curation Single-cell sequencing Tintinnid protozoal DNA ribosome DNA biodiversity ciliate classification DNA sequence evolution genetics phylogeny plankton Biodiversity Biological Evolution Ciliophora DNA, Protozoan DNA, Ribosomal Phylogeny Plankton Sequence Analysis, DNA Ciliated protists in the subclasses Choreotrichia and Oligotrichia are major components of marine plankton. Despite their ecological relevance, there are uncertainties in their systematics and diversity. We retrieved and curated all the GenBank ribosomal DNA (rDNA) sequences from these groups, which were analyzed in two ways. The first approach was based on morphologically-identified sequences (including those of two families and six genera newly studied here by single-cell sequencing), and aimed at improving phylogenetic inferences using concatenated sequences of three rDNA loci. Based on phylogenetic and morphological support, we update the taxonomic classification of these subclasses into 23 families, including the re-established Favellidae. We also propose an informal naming system for incertae sedis taxa, namely Tintinnopsis and five related genera that are spread among eleven lineages. The second approach included unidentified environmental sequences, and was used to explore potentially novel diversity in these subclasses. Our results support high proportions of both synonyms in tintinnids and uncharacterized taxa in choreotrichids and oligotrichs. One previously unidentified, environmental clade is here linked to our new Leegaardiellidae sequences. Our curation of almost 4000 rDNA sequences exemplifies known issues of public repositories, and suggests caution in both the use and contribution to these unique resources for evolutionary and diversity studies. © 2017 Elsevier Inc. Fil:Santoferrara, L.F. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_10557903_v112_n_p12_Santoferrara |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Ciliate Environmental sequencing Protist Sequence curation Single-cell sequencing Tintinnid protozoal DNA ribosome DNA biodiversity ciliate classification DNA sequence evolution genetics phylogeny plankton Biodiversity Biological Evolution Ciliophora DNA, Protozoan DNA, Ribosomal Phylogeny Plankton Sequence Analysis, DNA |
| spellingShingle |
Ciliate Environmental sequencing Protist Sequence curation Single-cell sequencing Tintinnid protozoal DNA ribosome DNA biodiversity ciliate classification DNA sequence evolution genetics phylogeny plankton Biodiversity Biological Evolution Ciliophora DNA, Protozoan DNA, Ribosomal Phylogeny Plankton Sequence Analysis, DNA Santoferrara, L.F. Alder, V.V. McManus, G.B. Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| topic_facet |
Ciliate Environmental sequencing Protist Sequence curation Single-cell sequencing Tintinnid protozoal DNA ribosome DNA biodiversity ciliate classification DNA sequence evolution genetics phylogeny plankton Biodiversity Biological Evolution Ciliophora DNA, Protozoan DNA, Ribosomal Phylogeny Plankton Sequence Analysis, DNA |
| description |
Ciliated protists in the subclasses Choreotrichia and Oligotrichia are major components of marine plankton. Despite their ecological relevance, there are uncertainties in their systematics and diversity. We retrieved and curated all the GenBank ribosomal DNA (rDNA) sequences from these groups, which were analyzed in two ways. The first approach was based on morphologically-identified sequences (including those of two families and six genera newly studied here by single-cell sequencing), and aimed at improving phylogenetic inferences using concatenated sequences of three rDNA loci. Based on phylogenetic and morphological support, we update the taxonomic classification of these subclasses into 23 families, including the re-established Favellidae. We also propose an informal naming system for incertae sedis taxa, namely Tintinnopsis and five related genera that are spread among eleven lineages. The second approach included unidentified environmental sequences, and was used to explore potentially novel diversity in these subclasses. Our results support high proportions of both synonyms in tintinnids and uncharacterized taxa in choreotrichids and oligotrichs. One previously unidentified, environmental clade is here linked to our new Leegaardiellidae sequences. Our curation of almost 4000 rDNA sequences exemplifies known issues of public repositories, and suggests caution in both the use and contribution to these unique resources for evolutionary and diversity studies. © 2017 Elsevier Inc. |
| format |
JOUR |
| author |
Santoferrara, L.F. Alder, V.V. McManus, G.B. |
| author_facet |
Santoferrara, L.F. Alder, V.V. McManus, G.B. |
| author_sort |
Santoferrara, L.F. |
| title |
Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| title_short |
Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| title_full |
Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| title_fullStr |
Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| title_full_unstemmed |
Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) |
| title_sort |
phylogeny, classification and diversity of choreotrichia and oligotrichia (ciliophora, spirotrichea) |
| url |
http://hdl.handle.net/20.500.12110/paper_10557903_v112_n_p12_Santoferrara |
| work_keys_str_mv |
AT santoferraralf phylogenyclassificationanddiversityofchoreotrichiaandoligotrichiaciliophoraspirotrichea AT aldervv phylogenyclassificationanddiversityofchoreotrichiaandoligotrichiaciliophoraspirotrichea AT mcmanusgb phylogenyclassificationanddiversityofchoreotrichiaandoligotrichiaciliophoraspirotrichea |
| _version_ |
1807322059173265408 |