Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae)

Luddington, Ian A.; Kaczmarska, Irena; Lovejoy, Connie

doi:10.1371/journal.pone.0045664

Cited by 61 publications

(42 citation statements)

References 48 publications

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“…Thus, Luddington et al. (), using the highly variable V4 region of the nuclear 18S rRNA, found that a threshold of 0.02 successfully separated 96.9% of species tested and Moniz and Kaczmarska (), using a class‐specific threshold of 0.11 with the 5.8S‐ITS2 as marker and uncorrected genetic distances, were able to separate 95% of the species tested. The ITS‐based p ‐distances between P. plurisecta and its closest relatives were found to be slightly higher than 0.02 and higher than the values obtained when the strains of P. cuspidata / P. pseudodelicatissima were compared to each other.…”

Section: Discussionmentioning

confidence: 99%

“…This point is discussed by Luddington et al. () concerning diatoms and can be extended to other taxonomic groups with pseudocryptic or cryptic species (e.g., Laza‐Martínez et al. ).…”

mentioning

confidence: 92%

“…Small parts of these regions have also been shown to be efficient barcodes for diatoms (Moniz and Kaczmarska , Luddington et al. ). Two regions of the rDNA cistrons were chosen for this study: the ITS and the LSU.…”

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confidence: 99%

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The genus Pseudo-nitzschia (Bacillariophyceae) in a temperate estuary with description of two new species: Pseudo-nitzschia plurisecta sp. nov. and Pseudo-nitzschia abrensis sp. nov.

Orive

Pérez-Aicua

David

et al. 2013

Journal of Phycology

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The genus Pseudo-nitzschia contains potentially toxic species of problematic taxonomy, making it one of the most intensively studied diatom genera. The study of 35 clonal strains isolated from the Bilbao estuary, an area that experiences recurrent blooms of Pseudo-nitzschia, revealed the presence of two new species, P. abrensis and P. plurisecta, differing from their congeners in both morphology and gene sequence. The morphological features were analyzed by LM and EM, whereas molecular analyses were based on the internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA. P. plurisecta appears closely related to P. cuspidata/P. pseudodelicatissima in the phylogenetic tree, whereas P. abrensis forms a moderately supported clade with P. heimii/P. subpacifica and P. caciantha/P. circumpora. Comparison of the secondary structure of ITS2 regions reveals marked differences in the most highly conserved regions among related taxa. Morphologically, the new species differ from their closest congeners in the arrangement of the poroid sectors and the density of valve striae and fibulae. The two species share similar pigment composition, and belong to the group of Pseudo-nitzschia species containing only chlorophyll c2 and c3 .

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Section: Discussionmentioning

confidence: 99%

“…This point is discussed by Luddington et al. () concerning diatoms and can be extended to other taxonomic groups with pseudocryptic or cryptic species (e.g., Laza‐Martínez et al. ).…”

mentioning

confidence: 92%

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The genus Pseudo-nitzschia (Bacillariophyceae) in a temperate estuary with description of two new species: Pseudo-nitzschia plurisecta sp. nov. and Pseudo-nitzschia abrensis sp. nov.

Orive

Pérez-Aicua

David

et al. 2013

Journal of Phycology

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“…However, the level of taxonomic placement, for example, from phylum level to ecotype, is completely dependent on the depth and accuracy of the reference databases. For this reason, alignment and placement within phylogenetic trees remain the best method for accurately portraying diversity within groups of closely related organisms (10). While amplicon sequencing shares some of the inherent biases of other PCR-based methods (11,12), it is useful for highlighting differences and similarities among samples, provided similar protocols are followed.…”

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confidence: 99%

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

Thaler

Lovejoy

2015

Appl Environ Microbiol

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Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes. Heterotrophic flagellates (HF) have a central role in marine food webs, particularly in the Arctic, where they can control phytoplankton biomass (1). Modeling studies indicate that they likely consume the majority of bacterial biomass in this region (2). In other marine environments, they have been found to be more important than viral lysis (3) or ciliate grazers (4) for controlling bacterial concentrations. HF range from pico-to nanosized cells (0.8 to 20 m) and are phylogenetically diverse, with representatives in most branches of the Eukaryota tree. Because taxon-specific differences in feeding behavior, population dynamics, and life histories may be important over broad ecosystem scales (5), the identification and quantification of the diverse groups can add substantially to our understanding of marine ecosystem function. However, HF taxa often have few diagnostic morphological features that enable easy identification (6) and microscopy-based studies rarely differentiate between HF taxonomic groups. Molecular approaches, such as cloning and amplicon sequencing, have provided additional information on the deep phylogenetic diversity of HF, especially in the Arctic (7). More recently, highthroughput multiplex tag sequencing of hypervariable regions of the 18S rRNA gene has become commonplace (8, 9). This is considered a semiquantitative method for retrievin...

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“…A number of examples have been published of species sharing sequences for a mitochondrial marker, although the problem is more widespread for 16S rDNA than for Cytochrome b or COI ([32], [16], [17]). 18S rDNA, while more useful for taxonomic assignment where no closely related sequences are available ([85], [86]) is more conserved than either 16S or COI in some taxonomic groups (table 3), and sometimes shows little or no divergence between some closely related species (table 3 and [82], [87]) distinguishable by mitochondrial markers (table 3 and [32]). When taking into account the error rates of the sequencing techniques, such low divergences can present serious pitfalls for differentiation of clades, as sequencing errors impose divergence thresholds to lower the risk of considering two clusters as distinct due solely to sequencing errors [88].…”

Section: Resultsmentioning

confidence: 99%

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

et al. 2012

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BackgroundResearchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.Methodology/Principal FindingsWe propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.Conclusions/SignificanceThis approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.

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Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae)

Cited by 61 publications

References 48 publications

The genus Pseudo-nitzschia (Bacillariophyceae) in a temperate estuary with description of two new species: Pseudo-nitzschia plurisecta sp. nov. and Pseudo-nitzschia abrensis sp. nov.

The genus Pseudo-nitzschia (Bacillariophyceae) in a temperate estuary with description of two new species: Pseudo-nitzschia plurisecta sp. nov. and Pseudo-nitzschia abrensis sp. nov.

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

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