The Molecular Age: microbial eukaryotes and transcriptomics

Despite influencing several biogeochemical, nutrient and atmospheric cycles, a vast number of marine microbial organisms, particularly marine eukaryotes are understudied, uncultivated or even undiscovered. Following the development and success of metagenomic and metatranscriptomic techniques, the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) was launched in 2010. Now 4 years later the assembled, functionally annotated and publicly available transcriptomes of over 650 marine eukaryotes have been published.

The nuclear genome can be difficult to sequence and assemble, thus transcriptomics was used as opposed to a genomic approach. A transcriptome can be described as the complement of mRNA transcribed from a cell's genome. Using the transcriptome has many advantages; it allows expressed genes to be identified and ommits intergenic regions, introns and repetitive DNA, whilst these can be interesting to study, they are found commonly in eukaryotes and can use a large proportion of sequencing resources. That said, the transcriptome is no substitute for the genome, both have advantages and disadvantages, therefore they should be used to complement eachother.

Most of the transcriptomes currently published are from the most abundant or ecologically important eukaryotes (mainly because these were the organisms researchers were working with). This is similar for other databases, for example many of the bacterial species which have biotechnological or biomedical applications are well-studied. In order to expand our breadth of knowledge of these organisms, I think a change in thought is needed. Surely, all organisms should to be studied? What is clear however, is the range of microbial eukaryote transcriptomes can only grow over time.

This project is an international project, involving academics from several universities and institutions. This can be both advantageous, in that the awareness of the project will grow more quickly and the workload shared, and disadvantageous, in that  the methodological approach may vary producing varied results. To combat this researchers used a universal protocol to reduce errors, this conferred greater comparibility of the data, and less need to reassemble contigs (overlapping sequences) or re-predict protein sequences to ensure consistency.

Already this project has provided information on interesting groups of microbial eukaryotes; haplosporidia, amoebozoans and heterotrophic flagellates to name a few. The groups which have some transcriptome records are shown below, represented by a red dot; 

It is evident that this project is more than a database, it provides a springboard for scientific investigation and has applications in a diverse range of fields; from physiology and ecology to taxonomy and evolutionary studies.They could function in conservation and population/epidemiological studies too. I think more 'databases' such as this should be set up for particular environments/organisms, whilst classical cultivation methods are still beneficial, a combination of both should be employed. 

Jack

References

Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, et al. (2014) The Marine Microbial EukaryoteTranscriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biol 12(6).

More information can be found at; www.marinemicroeukaryotes.org/