The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)

Marine microbial eukaryotes comprise a vast array of single-celled, nucleated microbes, including diatoms, dinoflagellates, amoebae, ciliates and water molds. These organisms fill numerous ecological roles ranging from photosynthetic primary producers (base of aquatic food webs) to heterotrophic consumers of pre-formed organic compounds. Despite their small size, they are responsible for generating up to half of the world’s oxygen.

Even though these organisms are abundant and ecologically important, the gene content of oceanic microbial eukaryotes has not been studied extensively. Therefore, one of the major goals of this Gordon and Betty Moore Foundation-funded project is to generate a catalog of expressed genes from approximately 700 such microbes. 686 samples representing 418 unique strains have been approved for inclusion in the project. All approved samples have had Illumina TruSeq libraries prepared and sequenced (Illumina Hi-Seq 2000 2x50-nt paired-end sequences) and transcriptomes assembled using a de bruijn graph based approach. Functional annotation was carried out based on searches against the PFam, SUPERFAMILY and TIGRFAMs HMM libraries as well as the UniProtKB/Swiss-Prot protein database. Raw sequence reads, transcriptome assemblies, annotations and metadata for 324 data sets are now publically available through CAMERA (http://camera.calit2.net/mmetsp/). The primary focus of this project is to increase the research community’s scientific knowledgebase and further analyses of complex marine communities. This will lead to a better understanding of the ecology and evolution of these highly diverse organisms.