Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea

Wang, Pu; Wang, Yurui; Wang, Chundi; Zhang, Tengteng; Al‐Farraj, Saleh A.; Gao, Feng

doi:10.1016/j.ympev.2017.04.018

Cited by 27 publications

(31 citation statements)

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“…Subsequently, using sequence information from multiple gene markers (18S‐ITS‐28S rDNA, alpha‐tubulin gene, COI, etc.) has become the widely‐accepted principle in phylogenetic analysis, especially for ciliates, an ecologically important protist group with a high degree of morphological complexity (Chen et al., ; Fernandes, da Silva Paiva, da Silva‐Neto, Schlegel, & Schrago, ; Gao, Gao, Wang, Katz, & Song, ; Gao & Katz, ; Gao, Song, & Katz, ; Gao, Li et al., ; Gao, Warren et al., ; Gao et al., ; Huang, Luo, Bourland, Gao, & Gao, ; Wang, Zhang et al., ; Wang, Wang et al., ; Wang, Wang, Sheng et al., ; Wang, Sheng et al., ; Yan et al., ; Yi, Huang, Yang, Lin, & Song, ; Zhang et al., ; Zhao et al., ).…”

Section: Introductionmentioning

confidence: 99%

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

Chen

Wang

Sheng

et al. 2018

Molecular Ecology Resources

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Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes is increasingly used to reconstruct the evolutionary history and classification of these microeukaryotes and thus provide a more robust framework for determining their systematics and diversity. More importantly, phylogenomic research usually requires high levels of hands-on bioinformatics experience. Here, we propose an efficient automated method, "Guided Phylogenomic Search in trees" (GPSit), which starts from predicted protein sequences of newly sequenced species and a well-defined customized orthologous database. Compared with previous protocols, our method streamlines the entire workflow by integrating all essential and other optional operations. In so doing, the manual operation time for reconstructing phylogenetic relationships is reduced from days to several hours, compared to other methods. Furthermore, GPSit supports user-defined parameters in most steps and thus allows users to adapt it to their studies. The effectiveness of GPSit is demonstrated by incorporating available online data and new single-cell data of three nonculturable marine ciliates (Anteholosticha monilata, Deviata sp. and Diophrys scutum) under moderate sequencing coverage (~5×). Our results indicate that the former could reconstruct robust "deep" phylogenetic relationships while the latter reveals the presence of intermediate taxa in shallow relationships. Based on empirical phylogenomic data, we also used GPSit to evaluate the impact of different levels of missing data on two commonly used methods of phylogenetic analyses, maximum likelihood (ML) and Bayesian inference (BI) methods. We found that BI is less sensitive to missing data when fast-evolving sites are removed.

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Section: Introductionmentioning

confidence: 99%

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

Chen

Wang

Sheng

et al. 2018

Molecular Ecology Resources

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“…Ciliated protists (ciliates) are important model organisms for studying molecular biology, cell biology, symbiotic relationships, ecology and evolution (Adl et al., ; Berger, ; Chen et al., ; Corliss, ; Gao, Song, & Katz, ; Lynn, ; Song, Warren, & Hu, ; Wang et al., ). One of the most diverse and systematically confused ciliate groups is the class Litostomatea Small & Lynn, 1981, which comprises two subclasses, Haptoria Corliss, and Trichostomatia Bütschli, 1889 (Lynn, ).…”

Section: Introductionmentioning

confidence: 99%

Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data

Huang

Zhang

et al. 2018

Zoologica Scripta

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Evolutionary relationships of taxa within the ciliate subclass Haptoria are poorly understood. In this study, we broaden the taxon sampling by adding 14 small subunit ribosomal RNA gene sequences, 13 large subunit ribosomal RNA gene sequences and 13 ITS1‐5.8S‐ITS2 gene sequences of haptorians. This includes the first molecular data from two genera, Pseudotrachelocerca Song, 1990, and Foissnerides Song & Wilbert, 1989. Phylogenies inferred from the three individual genes and concatenated data sets show that: (i) the subclass Haptoria could be a multiphyletic complex with about up to four main clades while “interrupted” by some intermingled with the related subclasses Rhynchostomatia, Trichostomatia and some incertae sedis; (ii) the genus Pseudotrachelocerca Song, 1990, is clearly separated from Litostomatea and clusters within an assemblage comprising the classes Prostomatea, Colpodea and Plagiopylea; (iii) both morphological evidence and molecular evidence indicate that the genus Foissnerides should be transferred from family Trachelophyllidae to Pseudoholophryidae; (iv) the validity of the order Helicoprorodontida Grain, 1994, and its monophyly is strongly supported; (5) the family Chaeneidae does not belong to the order Lacrymarida but represents a distinct clade in the subclass Haptoria.

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“…The most abundant mtSSU rDNA sequence of each of the 13 species was aligned together with other 80 sequences downloaded from National Center for Biotechnology Information (NCBI) database with MAFFT v.7 [53], a multiple alignment program for amino acid or nucleotide sequences, using data from Dunthorn et al, 2014 [32] and Wang et al, 2017 [29] as structural alignment examples. The phylogenetic analysis based on nSSU rDNA included 95 sequences in total, which were aligned with default parameters on the GUIDANCE2 Server [54].…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

“…Therefore, an increasing number of studies have sought additional/alternative gene markers that might perform better on microbial ecological research which focuses on species-level biodiversity, and better resolve ciliate evolution [29][30][31][32][33]. This is also due to the concerns about whether a single gene marker is sufficient to elucidate phylogenetic relationships [30,34,35], and nSSU rDNA might be too conserved to uncover cryptic species [36,37].…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, mitochondrial genes have the potential to be powerful gene markers as they exist in nearly all eukaryotes with a few exceptions [41] and can be reliably extracted from the organisms. In ciliates, mitochondrial genes are appreciated as an alternative gene marker that can effectively elucidate the systematic relationships within several classes of ciliates (e.g., Colpodea and Phyllopharyngea) as well as recover ciliate phylogeny at species level [29,32,[42][43][44]. However, these studies are rather scattered in certain species/a few clades, instead of shedding light on the whole phylum Ciliophora.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research

et al. 2020

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While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 104 to 8.1 × 105; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.

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Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea

Cited by 27 publications

References 50 publications

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data

Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research

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