Table 3.

Recent Application of Integrated “Omics” Approaches to Identify Genes Involved in Lipid Accumulation for Microalgal Biofuel Production

Organism	Objective	Key results	Reference
Nannochloropsis gaditana	To present a draft genome sequence and a genetic transformation method for the marine microalga N. gaditana	Genes required for glycerolipid biogenesis were identified in addition to genes specific to N. gaditana genome and those conserved across stramenopile lineage.	Radakovits et al., 2012
Chlamydomonas reinhardtii	To annotate glycerolipid biosynthesis genes based on similarity to homologs from Arabidopsis thaliana	Reconstruction of the major glycerolipid biosynthetic pathways. A novel BTA1Cr gene encoding a Chlamydomonas Betaine lipid synthase was identified and isolated.	Riekhof et al., 2005
C. reinhardtii	To analyze purified oil bodies by using proteomics approach	LC-MS/MS analysis identified 248 proteins of which 33 were putatively involved in lipid metabolism, particularly acyl- lipids and sterol. Besides the gene already known to regulate TAG biosynthesis in C. reinhardtii, 19 novel genes were predicted including acyltransferases, hydrolase/lipases, lipid trafficking proteins and proteins of sterol/ergosterol metabolism.	Nguyen et al., 2011
Cyanidioschyzon merolae	To study lipid biosynthetic pathway by genomic and biochemical analyses	Genes involved in the synthesis of fatty acids and lipids were identified. Genomic analysis indicated that C. merolae possess a standard pathway of biosynthesis of glycerolipids except for the absence of plant-type galactosyltransferase enzymes, which underlines the marked difference in lipid biosynthesis pathway between red algae and the green lineage.	Sato and Moriyama, 2007
Haematococcus pluvialis	To study the correlation between fatty acid synthesis and gene expression patterns under different stress conditions	Good correlation between ACP, KAS, FATA gene expression and fatty acid synthesis was observed. In response to stress treatment, the fatty acid synthesis was upregulated while there was no change in the quality of the synthesized fatty acids.	Lei et al., 2012
Diatom species including Thalassiosira pseudonana, Phaeodactylum tricornutum and Fragilariopsis cylindrus	To perform comprehensive in silico evaluation of the genes underlying the carbon metabolism pathways of diatoms	The study identified a total of 164 genes including 51 genes from T. pseudonana, 55 from P. tricornutum and 58 from F. cylindrus. Among them, the enzyme PFK was indicated to play a pivotal role in carbon metabolism and thus a potential target for genetic engineering to enhance biofuel production in microalgae. Further, subcellular localization of the putative enzymes demonstrated the lower half and upper half of glycolysis to be conserved in mitochondria and diatoms, respectively. The results highlight the significant role of intracellular trafficking in the regulation of carbon flux.	Smith et al., 2012
P. tricornutum	To study gene expression profiles during nutrient-deprivation and lipid-accumulation conditions	Genes/proteins up- and downregulated were identified. The potential role of carbon fixation pathways in lipid accumulation is also described.	Valenzuela et al., 2012
Chlorella	To study the distribution, domain structure, evolution and expressivity of autophagy genes (ATG) using genome-wide comparative analysis	The Chlorella genome was observed to encode all crucial ATG genes, which was further corroborated by expression profiles of the putative genes as determined by RT-PCR analysis. However, the receptor protein in cytoplasm-to-vacuole targeting and mitophagy were found to be absent in microalgae.	Jiang et al., 2012
Eukaryotic genomes (fifty-six species)	To examine desaturases and elongases by phylogenetics and motif structure prediction approaches	The predicted 275 desaturases and 265 elongases homologs were characterized into 4 and 2 distinct subfamilies, respectively. The resulting Hidden Markov Model profile can be applied to other comparative genomic studies for functional annotation of novel genes.	Hashimoto et al., 2008
Seven microalgal species including C. reinhardtii, T. pseudonana, P. tricornutum, C. merolae, Ostreococcus lucimarinus and O. tauri	To characterize the fatty acid desaturases on the basis of conserved histidine-rich motifs and phylogenetic profiles	67 desaturase genes were predicted and annotated along with reconstruction of the pathways involved in unsaturated fatty acid biosynthesis. A novel microsomal Δ12 desaturase was identified.	Chi et al., 2008
Dunaliella tertiolecta	To compare transcriptome and proteome of D. tertiolecta grown under N-replete and N-deplete conditions and high salt concentrations.	Several overexpressed genes and enzymes possibly involved in biosynthesis and catabolism of fatty acids, TAG and starch were discovered and the relevant pathways were reconstructed. Additionally, the pathways associated with biofuel precursor production were found to be interlinked to each other.	Rismani-Yazdi et al., 2011
Chlorella vulgaris UTEX 395	To demonstrate the utility of a transcriptome as a search model for proteomic analysis in an unsequenced microalga	Various genes and gene products involved in TAG biosynthetic pathway were identified.	Guarnieri et al., 2011
Five microalgal species including C. reinhardtii, Volvox carteri, O.lucimarinus, O. tauri and C. merolae	To perform comparative genomic analysis including subcellular localization, physicochemical characterization, exon-intron pattern, motif/ domain predictions of 398 putative lipid genes involved in lipid biosynthesis	The results indicated that although each of the algal species maintains the basic genomic repertoire required for lipid biosynthesis, they possess additional lineage-specific gene groups and the core lipid metabolic pathways in all the studied species are carried out by a comparable number of orthologous proteins.	Misra et al., 2012
Seven microalgal species including C. reinhardtii, V. carteri, O. lucimarinus, O. tauri, C. merolae, P. tricornutum, T. pseudonana	To perform sequence-structure analyses of plastid-located glycerol-3-phosphate acyltransferase (GPAT), a vital enzyme of TAG biosynthetic pathway	The phylogenetic tree along with motif and gene structure analyses indicated a close evolutionary relationship between red algae/diatom and green algae/plant lineages. Further subtle variation in amino acids of fatty acyl binding site were identified that might influence the substrate selectivity of GPAT.	Misra et al., 2013