Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms

Lee, Min-Ah; Faria, Daphne Georgina; Han, Moonsik; Lee, Juyun; Ki, Jang‐Seu

doi:10.1016/j.bse.2013.03.025

Cited by 21 publications

(14 citation statements)

References 54 publications

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“…Alverson et al (2011) demonstrated with molecular analysis that T. pseudonana has a freshwater Cyclotella ancestor and suggested that T. pseudonana is more appropriately classified by its original name, Cyclotella nana. Our phylogenetic analyses of several thalassiosiroid strains using 28S rDNA as a marker, clustered T. pseudonana as sister taxon of a group containing Cyclotella species, as in Alverson et al (2011) and Lee et al (2013), suggesting that T. pseudonana is a close relative of Cyclotella. However, the ITS tree built with several thalassiosiroid strains separated T. pseudonana and Cyclotella species into two different clades.…”

Section: Discussionmentioning

confidence: 77%

Molecular and morphological analyses of solitary forms of brackish Thalassiosiroid diatoms (Coscinodiscophyceae), with emphasis on their phenotypic plasticity

Hevia-Orube

Orive

David

et al. 2015

European Journal of Phycology

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Blooms of centric diatoms are a common feature in the Bilbao estuary during summer when river flow is at its lowest and water temperature is above 20ºC. To gain insight into the specific composition of these diatom blooms, net samples and cultures of estuarine isolates were analysed under the scanning electron microscope (SEM) and by molecular analyses of the Internal Transcribed Spacers 1 and 2 plus the coding region 5.8S (ITS region) and the 28S rRNA gene. Seven species of solitary centric diatoms belonging to four genera were found in the estuary including: Conticribra weissflogii, Cyclotella atomus var. atomus, Cyclotella cryptica, Cyclotella marina, Cyclotella meneghiniana, Discostella pseudostelligera and Thalassiosira pseudonana. Dominant species during blooms were C. meneghiniana and Co. weissflogii in the upper estuary and D. pseudostelligera and T. pseudonana in the middle estuary. The morphological traits used to differentiate between species pairs of similar morphology (C. meneghiniana/C. cryptica or D. pseudostelligera/D. woltereckii) were observed to vary with environmental conditions, denoting a great deal of phenotypic plasticity which would hinder accurate identification of the species when using morphological approaches alone.

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Section: Discussionmentioning

confidence: 77%

Molecular and morphological analyses of solitary forms of brackish Thalassiosiroid diatoms (Coscinodiscophyceae), with emphasis on their phenotypic plasticity

Hevia-Orube

Orive

David

et al. 2015

European Journal of Phycology

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“…) and is considered a good discriminatory molecular marker among centric diatom species (Lee et al. ). A gene fragment extending from the 5′ end of the 5.8S to the 3′ end of the helix III of ITS‐2 (5.8S + ITS‐2) has been proved to separate the 99.5% of diatom species (Moniz and Kaczmarska ).…”

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confidence: 99%

Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from theChaetoceros neogracilisspecies complex

Balzano

Percopo

Siano

et al. 2016

Journal of Phycology

102

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Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.

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“…; Lee et al. ). However, only 9 species, including 10 strains, from the available taxa were employed in the study by Tillmann et al.…”

Section: Discussionmentioning

confidence: 98%

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales)

Boopathi

Faria

Cheon

et al. 2015

J Eukaryotic Microbiology

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The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples.

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Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms

Cited by 21 publications

References 54 publications

Molecular and morphological analyses of solitary forms of brackish Thalassiosiroid diatoms (Coscinodiscophyceae), with emphasis on their phenotypic plasticity

Molecular and morphological analyses of solitary forms of brackish Thalassiosiroid diatoms (Coscinodiscophyceae), with emphasis on their phenotypic plasticity

Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from theChaetoceros neogracilisspecies complex

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales)

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