Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex

Miranda, Lilibeth; Zhuang, Yunyun; Zhang, Huan; Lin, Senjie

doi:10.1016/j.hal.2012.01.002

Cited by 62 publications

(59 citation statements)

References 65 publications

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“…The range of intra specific sequence variability observed in this study was in the range of 0.01-0.036 %, which is reasonable considering natural intra-specific variability and sequencing errors of NGS approaches (Behnke et al, 2011;Miranda et al, 2012). Overall, our data suggest that preservation with mercury chloride does not significantly impact the nucleotide composition of 18S sequences or qualitative information on community composition determined with molecular methods.…”

Section: Natural Pelagic Community and Mercury Chloride Preserved Trasupporting

confidence: 72%

Protist Communities in Moored Long-Term Sediment Traps (Fram Strait, Arctic)–Preservation with Mercury Chloride Allows for PCR-Based Molecular Genetic Analyses

et al. 2017

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Here we present a pilot study demonstrating, that preservation with mercury chloride allows the application of PCR-based molecular methods for the characterization of marine protist communities collected with moored long-term sediment traps. They can provide information on pelagic protist communities by collecting sinking plankton from the upper water column all year-round, even in remote polar oceans. Assessment of small protist species from the nano-and picoplankton fractions in sedimented material by microscopy is extremely challenging or almost impossible. Hence, comprehensive studies of variability in protist community composition in moored long-term sediment traps are scarce. Considering that marine nano-and picoeukaryotes are ecologically very important, new approaches are urgently needed to investigate protists in the smallest size-fractions of moored long-term sediment trap samples. We applied the quick and cost-effective the door for molecular genetic analyses of long-term sediment trap samples, and that PCR-based molecular methods have a strong potential to become an important tool for comprehensive taxonomic analyses of protist-and bacterial communities in moored long-term sediment traps.

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Section: Natural Pelagic Community and Mercury Chloride Preserved Trasupporting

confidence: 72%

Protist Communities in Moored Long-Term Sediment Traps (Fram Strait, Arctic)–Preservation with Mercury Chloride Allows for PCR-Based Molecular Genetic Analyses

et al. 2017

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“…The intragenomic variability of ribosomal cluster was also demonstrated in various groups of protists, for example, ciliates (Gong et al 2013), foraminifera (Pillet et al 2012) and dinoflagellates (Gribble and Anderson 2007;Miranda et al 2012). In Amoebozoa some SSU rRNA gene sequence variation between different molecular clones of the same amplicon does occur, and is usually detected by sequencing multiple clones of the PCR product amplified from the genomic DNA.…”

Section: Unusual Pattern Of Ssu Rrna Gene Variability In Ripellamentioning

confidence: 99%

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Kudryavtsev

Гладких

2017

European Journal of Protistology

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Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.

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“…The 97 % similarity level has shown to be the most suitable to reproduce original eukaryotic diversity (Behnke et al 2011) and has also the effect of bracing most of the sequencing errors (Kunin et al 2010). Furthermore, known intragenomic SSU polymorphism levels can range to 2.9 % in dinoflagellate species (Miranda et al 2012). OTUs comprised of only one sequence (singletons) were removed.…”

Section: Data Analysis 454-pyrosequencingmentioning

confidence: 99%

Protist community composition in the Pacific sector of the Southern Ocean during austral summer 2010

et al. 2013

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Knowledge about the protist diversity of the Pacific sector of the Southern Ocean is scarce. We tested the hypothesis that distinct protist community assemblages characterize large-scale water masses. Therefore, we determined the composition and biogeography of late summer protist assemblages along a transect from the coast of New Zealand to the eastern Ross Sea. We used state of the art molecular approaches, such as automated ribosomal intergenic spacer analysis and 454-pyrosequencing, combined with high-performance liquid chromatography pigment analysis to study the protist assemblage. We found distinct biogeographic patterns defined by the environmental conditions in the particular region. Different water masses harbored different microbial communities. In contrast to the Arctic Ocean, picoeukaryotes had minor importance throughout the investigated transect and showed very low contribution south of the Polar Front. Dinoflagellates, Syndiniales, and small stramenopiles were dominating the sequence assemblage in the Subantarctic Zone, whereas the relative abundance of diatoms increased southwards, in the Polar Frontal Zone and Antarctic Zone. South of the Polar Front, most sequences belonged to haptophytes. This study delivers a comprehensive and taxon detailed overview of the protist composition in the investigated area during the austral summer 2010.

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Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex

Cited by 62 publications

References 65 publications

Protist Communities in Moored Long-Term Sediment Traps (Fram Strait, Arctic)–Preservation with Mercury Chloride Allows for PCR-Based Molecular Genetic Analyses

Protist Communities in Moored Long-Term Sediment Traps (Fram Strait, Arctic)–Preservation with Mercury Chloride Allows for PCR-Based Molecular Genetic Analyses

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Protist community composition in the Pacific sector of the Southern Ocean during austral summer 2010

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