ITS2, 18S, 16S or any other RNA — simply aligning sequences and their individual secondary structures simultaneously by an automatic approach

Wolf, Matthias; Koetschan, Christian; Müller, Tobias

doi:10.1016/j.gene.2014.05.065

Cited by 71 publications

(62 citation statements)

References 42 publications

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“…1A,B; [29]). Building on this results and on previous studies [27]–[29], [31], [33], [70]–[73], the implementation of rRNA sequence-structure models is recommended for accurate phylogenetic estimates.…”

Section: Discussionmentioning

confidence: 69%

“…We employed both traditional phylogenetic methods using sequence data and recently developed tools to simultaneously infer alignments and phylogenies based on the primary sequence and the secondary structure information [31], [32], [33]. We analysed conserved structural elements of the ITS2 folding to pinpoint sequence-structure sinapomorphies supporting phylogenetic relationships between clades as well as sequence-structure autapomorphies distinctive to given terminal groups, valuable for their molecular diagnosis.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

2014

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The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

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Section: Discussionmentioning

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

2014

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“…Primary sequence information combined with their individual secondary structures increases the accuracy and robustness of the resulting phylogenetic tree (reviewed in Wolf et al. ()). Thus, the state of the art methodology recently described by Heeg and Wolf () was applied for the phylogenetic reconstruction of Chlorellaceae including the algal symbiont of T. utriculariae .…”

Section: Methodsmentioning

confidence: 99%

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant

Pitsch

Adamec

Dirren

et al. 2016

J Eukaryotic Microbiology

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The genus Tetrahymena (Ciliophora, Oligohymenophorea) probably represents the best studied ciliate genus. At present, more than forty species have been described. All are colorless, i.e. they do not harbor symbiotic algae, and as aerobes they need at least microaerobic habitats. Here, we present the morphological and molecular description of the first green representative, Tetrahymena utriculariae n. sp., living in symbiosis with endosymbiotic algae identified as Micractinium sp. (Chlorophyta). The full life cycle of the ciliate species is documented, including trophonts and theronts, conjugating cells, resting cysts and dividers. This species has been discovered in an exotic habitat, namely in traps of the carnivorous aquatic plant Utricularia reflexa (originating from Okavango Delta, Botswana). Green ciliates live as commensals of the plant in this anoxic habitat. Ciliates are bacterivorous, however, symbiosis with algae is needed to satisfy cell metabolism but also to gain oxygen from symbionts. When ciliates are cultivated outside their natural habitat under aerobic conditions and fed with saturating bacterial food, they gradually become aposymbiotic. Based on phylogenetic analyses of 18S rRNA and mitochondrial cox1 genes T. utriculariae forms a sister group to Tetrahymena thermophila.

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“…, , reviewed in Wolf et al. ). The tree was reconstructed by the neighbor joining (NJ) method, using ProfDistS v0.9.9 (Qt version; Friedrich et al.…”

Section: Methodsmentioning

confidence: 99%

“…Wolf et al. ). Bootstrap support (Felsenstein ) for the MP sequence‐structure tree was estimated based on 1,000 pseudoreplicates.…”

Section: Methodsmentioning

confidence: 99%

A non‐toxigenic but morphologically and phylogenetically distinct new species of Pseudo‐nitzschia, P. sabit sp. nov. (Bacillariophyceae)

Teng

Lim

et al. 2015

Journal of Phycology

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A new species of Pseudo-nitzschia (Bacillariophyceae) is described from plankton samples collected from Port Dickson (Malacca Strait, Malaysia) and Manzanillo Bay (Colima, Mexico). The species possesses a distinctive falcate cell valve, from which they form sickle-like colonies in both environmental samples and cultured strains. Detailed observation of frustules under TEM revealed ultrastructure that closely resembles P. decipiens, yet the new species differs by the valve shape and greater ranges of striae and poroid densities. The species is readily distinguished from the curve-shaped P. subcurvata by the presence of a central interspace. The morphological distinction is further supported by phylogenetic discrimination. We sequenced and analyzed the nuclear ribosomal RNA genes in the LSU and the second internal transcribed spacer, including its secondary structure, to infer the phylogenetic relationship of the new species with its closest relatives. The results revealed a distinct lineage of the new species, forming a sister cluster with its related species, P. decipiens and P. galaxiae, but not with P. subcurvata. We examined the domoic acid (DA) production of five cultured strains from Malaysia by Liquid chromatography-mass spectrometry (LC-MS), but they showed no detectable DA. Here, we present the taxonomic description of the vegetative cells, document the sexual reproduction, and detail the molecular phylogenetics of Pseudo-nitzschia sabit sp. nov.

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ITS2, 18S, 16S or any other RNA — simply aligning sequences and their individual secondary structures simultaneously by an automatic approach

Cited by 71 publications

References 42 publications

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant

A non‐toxigenic but morphologically and phylogenetically distinct new species of Pseudo‐nitzschia, P. sabit sp. nov. (Bacillariophyceae)

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