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Mol Plant. 2014 Feb;7(2):323-35. doi: 10.1093/mp/sst120. Epub 2013 Aug 21.

Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion.

Author information

1
CRIBI Biotechnology Centre, University of Padua, Padua 35121, Italy.

Abstract

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

PMID:
23966634
DOI:
10.1093/mp/sst120
[Indexed for MEDLINE]
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