Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

Abstract

BackgroundBiodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.ResultsNext generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta.ConclusionsThe construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.

Isolation and Characterization of Native Microalgae from the Peruvian Amazon with Potential for Biodiesel Production

“…The increase in total lipid content could be partially explained for a boost in transcript levels of genes encoding enzymes of the lipid biosynthesis pathways. According to this assumption, recent investigations showed that genes encoding the enzymes that catalyze the last step in the Kennedy pathway of triacylglycerol biosynthesis [81], such as glycerol-3-phosphate acyltransferase and acyl-glycerol-3-phosphate acyltransferase, are upregulated in response to nitrogen starvation [64,82,83]. Furthermore, the increase in total carbohydrate content can be explained by changes in the expression levels of genes involved in carbohydrate metabolism.…”

“…Furthermore, the increase in total carbohydrate content can be explained by changes in the expression levels of genes involved in carbohydrate metabolism. For example, when the oleaginous microalgae Neochloris oleoabundans is cultured under nitrogen starvation, the catabolic phase of starch, specifically α-amylase, which hydrolyzes starch to glucose, is strongly repressed [83]. …”

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

“…It is pertinent to note here that, despite the aforementioned progress in algal genomics, the rationale for sequencing these algal strains was not in the context of their lipid synthesis and hence, there still remains a paucity of biofuel-relevant genomic information (Blankenship, 2010;Rismani-Yazdi et al, 2011). The recently reported endeavours in algal transcriptome profiling have successfully demonstrated the feasibility of bypassing the bottleneck of genome sequencing and have improved our understanding of lipid metabolism in some unsequenced oleaginous microalgal species (Guarnieri et al, 2011;Rismani-Yazdi et al, 2011).…”

Microalgae Isolation and Selection for Prospective Biodiesel Production

“…Each micro-environment may provide algae strains with very different properties. As opposed to only manipulating a few individual cultured algae strains in the laboratory for high lipid productivity, a more efficient and useful strategy to identify oleaginous microalgae would be an in-depth and systematic investigation of a whole taxonomic group of microalgae over a wide geographical and ecological distribution [20]. By correlating this with algal oil contents and optimal environmental growth conditions, a predictive tool for selecting optimal microalgae strains for biofuel production maybe developed.…”