Taxonomic groups annotated

Groups with updated annotations

Division Class Who Date Status Version
Alveolata Apicomplexa J. del Campo 2019 Done 4.12
Alveolata Ciliates W. Ting, C. Bachy 2017 Done 4.7
Alveolata Ciliates V. Boscaro, L. Santoferrara, E. Gentekaki and Q. Zhang 2018 Done 4.11
Alveolata Dinoflagellates S. Mordret, D. Sarno 2018 Done 4.9
Rhizaria Collodaria T. Biard 2015 Done 2.0
Rhizaria Foraminifera R. Morard 2019 Planned
Rhizaria Radiolaria M. Mendez Sandin. 2019 Planned
Chlorophyta M.Tragin, A. Lopes dos Santos 2015 Done 3.0
Haptophyta B. Edvardsen 2015 Done 4.0
Stramenopiles R. Massana 2019 Done 4.12
Stramenopiles Diatoms (Chaetoceros) C. Gaonkar 2019 Done 4.12
Stramenopiles Bolidophyceae D. Vaulot 2017 Done 4.6
Stramenopiles Pelagophyceae D. Vaulot 2017 Done 4.6

List of references used to annotate database

Chlorophyta

  • Tragin, M., Lopes dos Santos, A., Christen, R., and Vaulot, D. (2016). Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect. Phycol. 3, 141–154. doi:10.1127/pip/2016/0059.
  • Lopes dos Santos A., Pollina T., Gourvil P., Corre E., Marie D., Garrido JL., Rodríguez F., Noël M-H., Vaulot D., Eikrem W. 2017. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Scientific Reports 7:14019. DOI: 10.1038/s41598-017-12412-5.

Ochrophyta

  • Adl, S.M., Bass, D., Lane, C.E., Lukeš, J., Schoch, C.L., Smirnov, A., Agatha, S. et al. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J. Eukaryot. Microbiol. 66:4–119.
  • Ichinomiya, M., dos Santos, A. L., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., et al. (2016). Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J. 10, 2419–2434. doi:10.1038/ismej.2016.38.
  • Derelle, R., López-García, P., Timpano, H. & Moreira, D. 2016. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (= Heterokonts). Mol. Biol. Evol. 33:2890–8.
  • Gaonkar, C.C., Piredda, R., Minucci, C., Mann, D.G., Montresor, M., Sarno, D. & Kooistra, W.H.C.F. 2018. Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae. PLoS One. 13:e0208929.
  • Massana, R., del Campo, J., Sieracki, M.E., Audic, S. & Logares, R. 2014. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. ISME J. 8:854–66.

Haptophyta

  • Edvardsen, B., Egge, E. S., and Vaulot, D. (2016). Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspect. Phycol. 3, 77–91. doi:10.1127/pip/2016/0052.

Ciliates

  • Agatha, S. and Strüder-Kypke, M.C. (2014) What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora). Acta Protozool. 2014: 7790.
  • Bachy, C., Gómez, F., López-García, P., Dolan, J.R., and Moreira, D. (2012) Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora). Protist 163: 873–887.
  • Boscaro V., Santoferrara L., Zhang Q., Gentekaki E., Syberg-Olsen M., del Campo J., Keeling P., 2018. EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates. Environmental Microbiology, 20: 2218-2230.
  • Santoferrara, L.F., Alder, V.V., and McManus, G.B. (2017) Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). Mol. Phylogenet. Evol. 112: 12–22.
  • Zhang, Q., Agatha, S., Zhang, W., Dong, J., Yu, Y., Jiao, N., and Gong, J. (2017) Three rDNA Loci-Based Phylogenies of Tintinnid Ciliates (Ciliophora, Spirotrichea, Choreotrichida). J. Eukaryot. Microbiol. 64: 226–241.

Dinoflagellates

  • Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, W.H.C.F. & Sarno, D. 2018. dinoref : A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol. Ecol. Resour. in press.

Apicomplexa

  • del Campo J., Heger TJ., Rodríguez-Martínez R., Worden AZ., Richards TA., Massana R., Keeling PJ. 2019. Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework. Frontiers in Microbiology 10:1–15. DOI: 10.3389/fmicb.2019.02373.

Plastids

  • Decelle, J., Romac, S., Stern, R.F., Bendif, E.M., Zingone, A., Audic, S., Guiry, M.D. et al. 2015. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour. 15:1435–144
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Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .

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