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...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autor principal: Santoferrara, Luciana F.
Publicado: 2017
Materias:
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
Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10557903_v112_n_p12_Santoferrara
http://hdl.handle.net/20.500.12110/paper_10557903_v112_n_p12_Santoferrara
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id paper:paper_10557903_v112_n_p12_Santoferrara
record_format dspace
spelling paper:paper_10557903_v112_n_p12_Santoferrara2023-06-08T16:03:13Z Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea) Santoferrara, Luciana F. 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. 2017 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10557903_v112_n_p12_Santoferrara 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, Luciana F.
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.
author Santoferrara, Luciana F.
author_facet Santoferrara, Luciana F.
author_sort Santoferrara, Luciana 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)
publishDate 2017
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10557903_v112_n_p12_Santoferrara
http://hdl.handle.net/20.500.12110/paper_10557903_v112_n_p12_Santoferrara
work_keys_str_mv AT santoferraralucianaf phylogenyclassificationanddiversityofchoreotrichiaandoligotrichiaciliophoraspirotrichea
_version_ 1768545611110416384

Ejemplares similares