Nannochloropsis genome and transcriptome
Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion.
The paper describes the genome sequence, gene annotation, and transcriptional profiling of the microalga Nannochloropsis gaditana B-31. The study identifies possible targets of genetic modification that could improve the yield of the strain for biodiesel production. The publication also reports the set up of a genome resource available online at www.nannochloropsis.org with multiple tools for information retrieval.
Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae. Here, we report a high-quality genomic assembly of Nannochloropsis gaditana, consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of the chromosomes. We identified 10646 complete genes and characterized possible alternative transcripts. The annotation of the predicted genes and the analysis of cellular processes revealed traits relevant for the genetic improvement of this organism such as genes involved in DNA recombination, RNA silencing, and cell wall synthesis. We also analyzed the modification of the transcriptional profile in nitrogen deficiency—a condition known to stimulate lipid accumulation. While the content of lipids increased, we did not detect major changes in expression of the genes involved in their biosynthesis. At the same time, we observed a very significant down-regulation of mitochondrial gene expression, suggesting that part of the Acetyl-CoA and NAD(P)H, normally oxidized through the mitochondrial respiration, would be made available for fatty acids synthesis, increasing the flux through the lipid biosynthetic pathway. Finally, we released an information resource of the genomic data of N. gaditana, available online at www.nannochloropsis.org.
KEYWORDS: Nannochloropsis, SOLiD, biofuel, chromosomes, de novo assembly, genome, lipids, nitrogen deprivation, telomeres., transcriptome