Resources for the study of living Retaria

This is intended to be a collaborative forum to share resources for the study of living Retaria, and to provide a basis for non-experts. One of the goals of the seminar series is to gain an overview of the current state of the research, trends, and potential future research prospects in these fascinating organisms. This page is intended as an evolving resource on multiple aspects of the biology of Retaria. At the moment this list is far from exhaustive. Any contribution is most welcome and very much appreciated, so we can achieve an exhaustive and up-to-date list of different tools and references to cover all disciplines studying living Retaria.

Arguably the diversity of Retaria is the most studied discipline, since it began with the Pioneering work of 19th-century naturalists such as Alcide D’orbigny and Hernst Haeckel. Their extreme usefulness has driven the study of these organisms as biostratigraphic markers and they have been the workhorse of industrial micropaleontology, which is why the typification of most extant species has been done of fossil material. The described diversity in fossils have been made available through websites such as microtax.

For the modern day diversity, several resources have been developed in recent years thanks to the development of high throughput techniques. The EcoTaxa website gathers a worldwide collection of in situ images collected mainly by flow imaging approaches, and the Protists Ribosomal Reference (PR2) database is a collection of all publicly available 18S phylogenetically curated rDNA sequences, which has been recently curated for Radiolaria and Foraminifera.

Lastly, EukProt is a recently developed database with predicted protein sets for the study of eukaryotic diversity, that might be handy for novel analysis of Retaria genomic and transcriptomic data. Lastly, PhyloFisher is a workflow for the automated reconstruction of phylogenomic trees.

The living ecology of Retaria is mostly inferred from biogeographical analysis of metabarcoding, that is the environmental sequencing of taxonomic markers (e.g., the V4 or V9 hypervariable regions of the 18S rDNA). Worldwide datasets such as the Tara Oceans and the Malaspina expeditions or the EukBank initiative, allow the detail characterization of biogeographic patterns on metabarcoding and metagenomics datasets.

The Ocean Atlas is a recently developed interactive tool for the exploration of biogeographic patterns in metabarcoding datasets (OBA) or gene expresion in metagenomic datasets (OGA) among others. The meta-PR2 is a similar tool that gathers several independent projects analyzed independently. These resources are very accessible for the non-expert and allow the production of publication ready plots. For more elaborate ecological analysis, the GUSTA ME website provides an excellent guide to statistical analysis in microbial ecology.

It is important to note that molecular barcodes do not intend to replace the more classical view of morphological species. Biases such as gene copy number, intragenomic variability or amplification/sequencing artifacts might provide a distorted view of the diversity compared to morphological approaches. This is specially important when focusing on Foraminifera, which its 18S rDNA is not sequenced with common primer-pairs and therefore its representation in global surveys might be biased.

Complementary to biogeographical information acquired via metabarcoding, recent databases have seen the light over the past years providing, for example for foraminifera, distribution (incl. abundances) of specimens per species globally in the plankton (FORCIS database) and at the surface of the sediments (FORCENS). The development of automated image recognition also allowed the publication of large reference images dataset (Endless forams).

There are few databases focusing on the interactions between protists, such as the Protists Interactions DAtabase (PIDA; although not maintained since 2018) or the recently created AquaSymbio.