Intraspecific Genetic Variation in <i>Paramecium</i> Revealed by Mitochondrial Cytochrome <i>c</i> Oxidase I Sequences

Barth, Dana; Krenek, Sascha; Fokin, Sergei I.; Berendonk, Thomas U.

doi:10.1111/j.1550-7408.2005.00068.x

Cited by 150 publications

(147 citation statements)

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“…Our chosen primers seemed to be too constricted, and marker genes of several strains could not be amplified. In diatoms, different COI primers were used for raphid pennates and centric diatoms (evans et al 2007); in fact, different COI primers were even needed for different ciliate genera (Barth et al 2006;lynn et al 2006).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity in chrysophytes: Comparison of different gene markers

Böck¹,

Chatzinotas²,

Boenigk³

2017

Fottea

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Abstract:Chrysophytes are a diverse group of protists belonging to the Stramenopiles. They encompass a broad range of nutrition strategies (phototrophy, mixotrophy and heterotrophy) and morphological forms (unicellular, colonial, branched, non-scaled to silica-scaled). However, taxonomy, identification and delineation of genera and species are hampered by the polyphyletic origin of several morphotypes and the low resolution of morphological features; moreover, description of these features requires in many cases special equipment like TEM or SEM. To test the congruent phylogeny, genetic resolution and to reveal the genetic diversity of chrysophytes, we evaluated in this study different gene markers, in particular SSU and LSU rRNA genes, ITS, and COI in terms of phylogenetic clustering, separation of phylogenetic lineages and genetic distances within and between clades. Our results showed that the general topology of the SSU rRNA gene phylogeny is similar to that of the LSU rRNA gene phylogeny, with a higher genetic divergence for the latter. The topology of the COI phylogeny differed from the ribosomal data, and showed the highest genetic divergence within groups and between groups for all compared markers. The 5.8S rRNA gene offered only a limited phylogenetic resolution with low genetic divergence. ITS showed a high genetic divergence, but phylogenetic analyses were hampered by high variance in sequence lengths between clades.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity in chrysophytes: Comparison of different gene markers

Böck¹,

Chatzinotas²,

Boenigk³

2017

Fottea

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“…Although mainly based on animals, the potential use of COI marker as a barcoding tool was also demonstrated for several groups of protist (Barth et al 2006;Chantangsi et al 2007;Lin et al 2009;Nassonova et al 2010) and red algae (Saunders 2005). However, COI sequences are available for relatively few groups of eukaryotes.…”

Section: Discussionmentioning

confidence: 99%

“…Such problems were also reported in other groups of protists. In ciliates and diatoms, the developed COI primers work also for a limited number of genera (Barth et al 2006;Chantangsi et al 2007;Chantangsi and Lynn 2008;Guggiari and Peck 2008;Lynn and Strüder-Kypke 2006). More universal primers need to be developed in order to use this barcoding approach for all Euglyphida, and perhaps for the Rhizaria in general.…”

Section: Limitations Of the Primers Usedmentioning

confidence: 99%

“…This stresses the need of testing any potential barcode for species delimitation before utilizing the genetic marker in contingent research (e.g., a study on biogeography or paleoecology). Some recent studies have demonstrated the usefulness of the COI for species identification in different groups of microbial eukaryotes, such as ciliates (Barth et al 2006;Chantangsi et al 2007;Chantangsi and Lynn 2008), diatoms (Evans et al 2007;Evans et al 2008; Evans and Mann 2009), dinoflagellates (Lin et al 2009) and amoebozoans (Nassonova et al 2010). The utility of the COI marker for species level discrimination and phylogenetic inferences has yet to be tested within a member of the Rhizaria, the eukaryotic supergroup to which the euglyphid testate amoebae belong.…”

Section: Introductionmentioning

confidence: 99%

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Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida)

Heger

Pawłowski

Lara

et al. 2011

Protist

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The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to six Cyphoderia morphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500 bp) was much shorter than the SSU sequences (1600 bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.

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“…The advantage of the COI-based metabarcoding approach is to provide a much finer level of taxonomic resolution than that the SSU rRNA gene usually used in environmental DNA studies. COI has also been shown to give high taxonomic resolution in many microbial eukary-otic groups (Barth et al 2006;Chantangsi et al 2007;Heger et al 2010;Lin et al 2009;Nassonova et al 2010). For exam-ple, in the Hyalospheniidae, SSU rRNA does not allow to discriminating among closely related taxa (Lara et al 2008) while COI does (Kosakyan et al 2012(Kosakyan et al , 2013.…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

Kosakyan

Mulot

Mitchell

et al. 2015

European Journal of Protistology

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Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.

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Intraspecific Genetic Variation in Paramecium Revealed by Mitochondrial Cytochrome c Oxidase I Sequences

Cited by 150 publications

References 36 publications

Genetic diversity in chrysophytes: Comparison of different gene markers

Genetic diversity in chrysophytes: Comparison of different gene markers

Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida)

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

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