Genomic insights from the oleaginous model alga Nannochloropsis gaditana

Abstract

Nannochloropsis species have emerged as leading phototrophic microorganisms for the production of biofuels. Several isolates produce large quantities of triacylglycerols, grow rapidly, and can be cultivated at industrial scales. Recently, the mitochondrial, plastid and nuclear genomes of Nannochloropsis gaditana were sequenced. Genomic interrogation revealed several key features that likely facilitate the oleaginous phenotype observed in Nannochloropsis, including an over-representation of genes involved in lipid biosynthesis. Here we present additional analyses on gene orientation, vitamin B12 requiring enzymes, the acetyl-CoA metabolic node, and codon usage in N. gaditana. Nuclear genome transformation methods are established with exogenous DNA integration occurring via either random incorporation or by homologous recombination, making Nannochloropsis amenable to both forward and reverse genetic engineering. Completion of a draft genomic sequence, establishment of transformation techniques, and robust outdoor growth properties have positioned Nannochloropsis as a new model alga with significant potential for further development into an integrated photons-to-fuel production platform.

Keywords: Nannochloropsis; algae; biofuels; genomics; lipids.

Figure 1. Selected lipid metabolism genes as a fraction of total genes. The number of gene homologs involved in lipid metabolism in each genome was normalized to the total number of genes in each organism. Total gene models in each organism: N. gaditana, 9,052; E. siliculosus, 16,256; P. tricornutum, 10,402; C. reinhardtii, 15,143.

Figure 2. (A) Distance in nucleotides between Nannochloropsis gaditana gene models in relation to gene orientation. (B) A schematic phylogenetic tree of stramenopiles and other closely related eukaryotes, and a heat map indicating the percentage of genes with the specified relative orientation (diverging, converging, or same) to neighboring genes in the given organisms. Genes that are randomly oriented with respect to each other would be evenly distributed at 25% of genes in each orientation.

Figure 3. Codon utilization in N. gaditana shown by relative adaptiveness, wij, which is defined as the ratio of the number of occurrences, xij, of a codon, j, for a given amino acid, i, compared with the number of occurrences of the codon used with the highest frequency for that amino acid, ximax, or wij = 100 * xij / ximax.30 Codon use was analyzed for 8,642 genes comprising more than 3 million codons.