Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae

Abstract

The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity

“…Gaonkar et al . () showed that a phylogeny inferred from the V4 region of Chaetocerotaceae corroborates those inferred from the 18S and partial 28S rDNA regions and that virtually all species are distinguishable. Species identification of the inferred taxa is also straightforward because of the availability of an extensive 18S rDNA reference sequence database (for morphology of the reference strains, see Supporting Information figs.…”

“…Species identification of the inferred taxa is also straightforward because of the availability of an extensive 18S rDNA reference sequence database (for morphology of the reference strains, see Supporting Information figs. 1–44 of Gaonkar et al ., ; see also e.g., Balzano et al ., ; Li et al ., ). We compared phylogenetically inferred taxa with OTUs obtained using clustering to explore how the two methods perform.…”

“…Our study site is the Long‐Term Ecological Research station MareChiara (LTER‐MC) in the Gulf of Naples (GoN; Mediterranean Sea). Phytoplankton diversity and its seasonal cycling have been studied there extensively since 1984 (Zingone et al ., ) and so has the chaetocerotacean diversity (Kooistra et al ., ; Gaonkar et al ., ). A first metabarcode survey carried out on eight sampling dates in 2011, using the V4 region as marker (Piredda et al ., ), revealed high chaetocerotacean abundance.…”

“…The present metabarcoding study focuses on species delineation and identification within the two extant genera Chaetoceros and Bacteriastrum (e.g., Balzano et al ., ; Li et al ., ; Gaonkar et al ., ) of the planktonic diatom family Chaetocerotaceae (De Luca et al ., ). Many of its species are common and widespread (Hasle and Syvertsen, ; De Luca et al ., ) and constitute major drivers of carbon and silica sinking (Treguer et al ., ).…”

Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

“…Gaonkar et al. ) and, where possible, to identify diagnostic morphological features. In this way, our results feed directly into the international open‐access barcoding library Diat.barcode (Rimet et al.…”