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Jan 03

First article published in the open access journal Protist Genomics

Protist Genomics (PG) has just published its first research article: Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa teneraChilodonella uncinata, and Subulatomonas tetraspora. By Jessica Grant, Daniel Lahr, Federico Rey, Gordon Burleigh, Jeffrey Gordon, Rob Knight, Robert Molestina and Laura Katz.

Grant and collaborators present and describe new sequence data from three interesting protists. The data was generated through the technique called RNA-seq, which involves the preparation of a cDNA library our of poly-A enriched total cellular RNA (i.e. mostly mRNA) and subsequently ‘massively’ sequencing using one of the different types of ‘Next generation’ DNA sequencing available, in this case the authors used pyrosequencing (Roche-454).

The goals of the study are twofold. First, to provide the community with valuable expressed sequence data of these three poorly known protist species, each with great potential to illuminate questions on eukaryotic evolution. The second aim was to share with the community the author’s experience at dealing with the technical difficulties of working with very difficult culture conditions. In all cases the organisms cannot be grown without the presence of large amounts of diverse bacteria, which poses severe complications for the preparation of RNA and subsequent bioinformatic analyses. The methodological details provided in the article should be read by anyone working on similar studies with difficult samples.

Corallomyxa tenera is an amoeba-like protist belonging to the supergroup Rhizaria. This eukaryotic supergroup is the least studied from a genomic perspective, therefore the data presented by Grant et al. will result particularly useful in large-scale phylogenetic analyses involving diverse eukaryotic lineages.

Chilodonella uncinata belongs in the Ciliophora, whose members are typically referred to as ‘ciliates’. Two ciliates (Paramecium and Tetrahymena) are widely used as laboratory models and have their genomes sequenced and analysed thoroughly. However, they are closely related, thus offering limited insight into the molecular diversity of the whole group. In addition to providing tools to study this particular species, the data from C. uncinata will also prove useful to study deeper relationships among ciliates and alveolates.

Subulatomonas tetraspora has been recently described from anoxic marine sediments. It is a small amoeboflagellate, and thus far, phylogenetic analyses placed it outside of the known major groups of eukaryotes. Sequence data from S. tetraspora and other relatives are going to be critical to determine whether they conform a new eukaryotic supergroup.