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Background  Microalgae have received considerable interest as a source of biofuel production. The unicellular green alga  Pseudochoricystis ellipsoidea  (non-validated scientific name) strain Obi appears to be suitable for large-scale cultivation in outdoor open ponds for biodiesel production because it accumulates lipids to more than 30 % of dry cell weight under nitrogen-depleted conditions. It also grows rapidly under acidic conditions at which most protozoan grazers of microalgae may not be tolerant. The lipid productivity of this alga could be improved using genetic engineering techniques; however, genetically modified organisms are the subject of regulation by specific laws. Therefore, the aim of this study was to develop a self-cloning-based positive selection system for the breeding of  P. ellipsoidea .    Results  In this study, uracil auxotrophic mutants were isolated after the mutagenesis of  P. ellipsoidea  using either ultraviolet light or a transcription activator-like effector nuclease (TALEN) system. The cDNA of the uridine monophosphate synthase gene ( PeUMPS ) of  P. ellipsoidea  was cloned downstream of the promoter of either a beta-tubulin gene ( PeTUBULIN1 ) or the gene for the small subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase ( PeRBCS ) to construct the pUT1 or pUT2 plasmid, respectively. These constructs were introduced into uracil auxotroph strains, and genetically complementary transformants were isolated successfully on minimal agar plates. Use of Noble agar as the solidifying agent was essential to avoid the development of false-positive colonies. It took more than 6 weeks for the formation of colonies of pUT1 transformants, whereas pUT2 transformants formed colonies in 2 weeks. Real-time PCR revealed that there were more  PeUMPS  transcripts in pUT2 transformants than in pUT1 transformants. Uracil synthesis (Ura + ) transformants were also obtained using a gene cassette consisting solely of  PeUMPS  flanked by the  PeRBCS  promoter and terminator.    Conclusions  A self-cloning-based positive selection system for the genetic transformation of  P. ellipsoidea  was developed. Self-cloned  P. ellipsoidea  strains will require less-stringent containment measures for large-scale outdoor cultivation.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0277-0) contains supplementary material, which is available to authorized users.

Construction of a self-cloning system in the unicellular green alga Pseudochoricystis ellipsoidea