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Background  Microalgae-derived biodiesel is a promising substitute for conventional fossil fuels. In particular, the green alga  Chlorella protothecoides  sp. 0710 is regarded as one of the best candidates for commercial manufacture of microalgae-derived biofuel. This is due not only to its ability to live autotrophically through photosynthesis, but also to its capacity to produce a large amount of biomass and lipid through fermentation of glucose. However, until the present study, neither its genome sequence nor the platform required for molecular manipulations were available.    Results  We generated a draft genome for  C. protothecoides , and compared its genome size and gene content with that of  Chlorella variabilis  NC64A and  Coccomyxa subellipsoidea  C-169. This comparison revealed that  C. protothecoides  has a reduced genome size of 22.9 Mbp, about half that of its close relatives. The  C. protothecoides  genome encodes a smaller number of genes, fewer multi-copy genes, fewer unique genes, and fewer genome rearrangements compared with its close relatives. In addition, three  Chlorella -specific hexose-proton symporter (HUP)-like genes were identified that enable the consumption of glucose and, consequently, heterotrophic growth. Furthermore, through comparative transcriptomic and proteomic studies ,  we generated a global perspective regarding the changes in metabolic pathways under autotrophic and heterotrophic growth conditions. Under heterotrophic conditions, enzymes involved in photosynthesis and CO 2  fixation were almost completely degraded, either as mRNAs or as proteins. Meanwhile, the cells were not only capable of quickly assimilating glucose but also showed accelerated glucose catabolism through the upregulation of glycolysis and the tricarboxylic acid (TCA) cycle. Moreover, the rapid synthesis of pyruvate, upregulation of most enzymes involved in fatty acid synthesis, and downregulation of enzymes involved in fatty acid degradation favor the synthesis of fatty acids within the cell.    Conclusions  Despite similarities to other  Chlorella ,  C. protothecoides  has a smaller genome than its close relatives. Genes involved in glucose utilization were identified, and these genes explained its ability to grow heterotrophically. Transcriptomic and proteomic results provided insight into its extraordinary ability to accumulate large amounts of lipid. The  C. protothecoides  draft genome will promote the use of this species as a research model.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-582) contains supplementary material, which is available to authorized users.

Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes