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Problematic Biases in the Availability of Molecular Markers in Protists: The Example of the Dinoflagellates

100%

Gómez F.

Acta Protozoologica

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2014

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vol. 53

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issue 1

PL

Dinoflagellates (Alveolata, Dinophyceae) are protists with a truly remarkable diversity in lifestyles (free-living, parasites and mutualistic symbionts), habitats (marine, freshwater, plankton, benthos), and trophic modes (heterotrophic, plastid-containing). Here dinoflagellates are used to evaluate biases in the availability of molecular markers in relation to the variety of functional and ecological characteristics of protists. A large number of dinoflagellate sequences are available in GenBank, at least one for 56% of the 264 described genera. The most common marker is the small ribosomal subunit ribosomal DNA (49%). At the species level, SSU rDNA or the large subunit rDNA are available for 15% of the 2,386 described species. Availability of sequences of the internal transcribed spacers (ITS) and cytochrome oxidase I (COI) show a strong bias towards cultivable species. Relative to trophic mode, while about half of the known dinoflagellates are heterotrophic, only 12% of them have been sequenced compared to 29% of the plastid-containing species. For the COI marker availability is 10 times greater for plastid-containing compared to heterotrophic species. Freshwater species are underrepresented (13%) relative to the marine forms (22%). A high proportion of benthic species have been sequenced (46%) reflecting interest in Symbiodinium and harmful epiphytic taxa. Most of the relatively few described mutualistic species have been sequenced (> 80%). In contrast, only 17% of the described parasitic species have been sequenced, and most of the available sequences were not identified at the species level. In recent years, new species have been described mostly from coastal blooms or cultures. These studies are favored by the availability of abundant material for detailed studies of ultrastructure and multi-gene molecular phylogenies. Many methods are difficult to apply for the scarce specimens available from the open ocean. The requirement of these protocols, easy to apply with cultured species, is an obstacle in our knowledge of the open ocean diversity because it discourages studies based on sparse material. Consequently, in recent years descriptions of new species from the open ocean have declined considerably.

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Detection of Prorocentrum shikokuense in the Mediterranean Sea and evidence that P. dentatum, P. obtusidens and P. shikokuense are three different species (Prorocentrales, Dinophyceae)

51%

Gómez F., Zhang H., Roselli L., Lin S.

Acta Protozoologica

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2021

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vol. 60

47-59

EN

A dinoflagellate identified as Prorocentrum dentatum, P. shikokuense or P. donghaiense is responsible of massive harmful events. Blooms of a species identified as P. shikokuense have been recently reported in the Mediterranean Sea, and an exotic origin, tentatively introduced by ballast waters from Asia, has been hypothesized. The molecular data based on the small-, large subunit, and internal transcriber spacers ribosomal RNA gene (SSU-, LSU-, ITS rRNA) sequences confirmed P. shikokuense in the Mediterranean Sea. The Mediterranean ribotype is identical to a subtropical North Atlantic ribotype, and with slight divergence from the numerous sequences from the Pacific Ocean. To revisit the relationship between P. shikokuense (=P. donghaiense) and P. obtusidens, we provide the first micrographs of P. dentatum and P. obtusidens, the latter collected from the type locality. Our observations indicate that P. dentatum, P. obtusidens, and P. shikokuense are three different species. Their diagnostic morphological characters are: Prorocentrum dentatum is 44–60 μm long, leaf-shaped, pointed and central posterior end, conspicuous anterior shoulder; P. obtusidens is 33–41 μm long, irregular parallelepiped, almost paralel valve margins, eccentric and pointed posterior end, moderate anterior shoulder; and P. shikokuense is <25 μm long, sunflower seed-shaped, round and centric posterior end, inconspicuous anterior shoulder.

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Molecular Phylogeny of the Sand-dwelling Dinoflagellates Amphidiniopsis hirsuta and A. swedmarkii (Peridiniales, Dinophyceae)

51%

Gómez F., López-Medina L., Moreira D.

Acta Protozoologica

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2011

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vol. 50

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issue 3

PL

Amphidiniopsis is one of the most specious genera of sand-dwelling dinoflagellates. However, its systematic position and the affinities to other genera remain unresolved. We obtained the first SSU rDNA sequences of two species of Amphidiniopsis, A. hirsuta and A. swedmarkii collected from the French coasts of the English Channel. In the corresponding SSU rDNA phylogeny, the sand-dwelling Amphidiniopsis spp., Thecadinium dragescoi, Herdmania litoralis and the planktonic Archaeperidinium (= Protoperidinium) minutum formed a strongly supported clade (100% bootstrap support), with a Scrippsiella-like species occupying a basal position. This clade branched close to families of Peridiniales such as Calciodinellaceae (Scripssiella), Podolampadaceae (Podolampas, Roscoffia), Heterocapsaceae (Heterocapsa) and other peridinioids. The members of the clade of Amphidiniopsis are placed in the family Amphidiniopsidaceae, within the Peridiniales.

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1 Roselli L.

1 Zhang H.

Problematic Biases in the Availability of Molecular Markers in Protists: The Example of the Dinoflagellates

Detection of Prorocentrum shikokuense in the Mediterranean Sea and evidence that P. dentatum, P. obtusidens and P. shikokuense are three different species (Prorocentrales, Dinophyceae)

Molecular Phylogeny of the Sand-dwelling Dinoflagellates Amphidiniopsis hirsuta and A. swedmarkii (Peridiniales, Dinophyceae)