De novo genome sequencing of Skeletonema marinoi and Surirella brebissonii Mats Töpel¹*, Magnus Alm Rosenblad¹, Ulrika Lind¹, Susanna Gross², Sandra Karlsten¹, Jens Persson¹, Mattias Backman¹, Anna Godhe², Anders Blomberg¹ 1. Department of Chemistry and Molecular Biology, University of Gothenburg 2. Department of Biology and Environmental Sciences, University of Gothenburg *mats@topel.se Introduction De novo whole genome sequencing of the two diatom species Suri- rella brebissonii (CCMP2919) and Skeletonema marinoi (GUMACC St54) are currently conducted as part of the Linnaeus Centre for Marine Evolutionary Biology (CeMEB) initiative at the University of Gothenburg. This work is part of the Infrastructure for Marine Genetic model Organisms (IMAGO) project, aimed at developing new marine model systems and provide genomic and genetic tools to study vital phenomena and components of coastal marine ecosystems. Protein translocation in diatoms A chloroplast’s genome only encodes ~100 proteins, but the organ- elle requires many more proteins in order to perform its functions in the cell. Translocons at the Outer and Inner Chloroplast enve- lope membranes (TOC and TIC, respectively) are the two multi- protein complexes in plants, red- and green algae that enable chlo- roplasts to import these essential nuclear-encoded proteins. Diatom plastids, on the other hand, are surrounded by four mem- branes where the outermost is continuous with the endoplasmic reticulum (ER) [8]. The second membrane (known as the periplas- tid membrane [PPM]) is the remnant of the secondary endosymbiont’s plasma membrane (proposed to be of red algal origin) [9]. The two innermost membranes are homologous to the outer and inner envelope membranes in plant plastids and are de- rived from the membranes surrounding the cyanobiont of primary plastids [10]. The identity of the TOC and TIC translocons in diatoms and most other chromalveolate organism groups (e.g brown algae, dinofla- gellates and apicomplexan parasites) is mainly unknown. How- ever, bioinformatics analyses of whole genome sequences from dia- toms has shown that these systems are also present in diatoms. Bullman et al. [11] reported the discovery of an Omp85 protein that is localized in the third outermost plastid membrane (homologous to the outer envelope membrane in plants) of the diatom Phaeodactylum tricornutum. To date, this Omp85 protein is the only reported putative member of the TOC complex in diatoms. Our phylogenetic analyses (including bacterial, plant and diatom sequences) reveals that the diatom sequences are of red algal origin and more specifically belongs to the Toc75 gene family. Unexpectedly long branches in the diatom part of the tree indicates a rapid, albeit even, evolu- tionary rate. This phenomenon has been reported on previously, but the significance of the phenomenon has not yet been thor- oughly investigated. Assembly statistics DNA libraries (insert size 150 and 3000 bp), of which one were gen- erated from an axenic culture, and one RNA library (300 bp) from Surirella brebissonii has been sequenced. One axenic 300 bp library from Skeletonema marinoi has been generated. Both genomes have been assembled using the CLC de novo assembler software package. Sequence reads where preprocessed using cutadapt [1] and the fastx toolkit [2] (for details see http://matstopel.se/notebook). Skeletonema Surirella Total nt sequenced (Gb) 33 46 Total input to assembly (Gb) 26 33 Assembly size (Mb) 49 136 Number of contigs (K) 53 244 Average coverage (x/cont) 443 207 N50 (bp) 1673 694 Average contig lenght (bp) 929 557 Longest contig (Kb) 506* 76 *Putative bacterial symbiont. Preliminary findings Organelles − The plastid of Surirella brebissonii contains a group II intron with an ORF, the first group II intron to be identified in dia- toms. Interestingly, the mitochondrial genome of S. brebissonii has lost the group II intron present in both Thalassiosira pseudonana and Phaeodactylum tricornutu