dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

Abstract

Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity.

Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)

“…It might be only a matter of time until this particular taxonomic confusion is corrected for future releases of the SILVA databases, as this error has been already corrected in the dinoref database (Mordret et al, 2018). Therefore, the correct species name for the OTUs is (probably) freshwater Apocalathium aciculiferum.…”

“…Such powerful and continuously curated databases are scarce for protists, which are too small for direct observation and need microscopic expertise for examination. However, the problem is recognised, and considerable efforts have been made to build curated sequence databases and reference phylogenetic trees for dinophytes (Del Campo et al, 2018;Elferink et al, 2017;Mordret et al, 2018;Quast et al, 2013) and other microbial taxa.…”

“…Therefore, the correct species name for the OTUs is (probably) freshwater Apocalathium aciculiferum. It might be only a matter of time until this particular taxonomic confusion is corrected for future releases of the SILVA databases, as this error has been already corrected in the dinoref database (Mordret et al, 2018). The latter, in turn, relies on SSU reference sequence data only and is therefore unable to place environmental OTUs of studies using LSU (Elferink et al, 2017) and/or ITS sequences (Lutz, McCutcheon, McQuaid, & Benning, 2018).…”

“…Much progress has been made in the past years to build such DNAbarcoding databases, not only for animals and plants (Hollingsworth, 2011;Vernooy et al, 2010), but also for various microorganisms (Quast et al, 2013) such as fungi, diatoms, and dinophytes (Del Campo et al, 2018;Fourtanier & Kociolek, 2009;Mordret et al, 2018;Peršoh, 2015;Schoch et al, 2012;Stern et al, 2012).…”

Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding

“…Loci tested for dinoflagellates include the nuclear small ribosomal subunit (18S rRNA) ), large ribosomal subunit (28S rRNA; D1/D2 region) (Elferink et al 2017), internal transcribed spacers (Stern et al 2012) and the mitochondrial cytochrome c oxidase subunit I and cytochrome b (Lin et al 2009). The mitochondrial genes cannot be easily amplified from all dinoflagellate taxa (Stern et al 2012) and, amongst the nuclear loci, 18S rRNA remains the most well-sequenced marker in public databases due to their widespread use in dinoflagellate systematics (Mordret et al 2018).…”