Thesis

Lipid Metabolism Profile of E.huxleyi versus other Phytoplankton Species: A Comparative Study

The main aim of this study was to comparatively study the presence and expressions of lipid metabolism proteins in E.huxleyi and three other Prymnesiophyceae species G.oceanica, I.galbana, and Chryosochomulina. The proteins related lipid metabolism of E.huxleyi were downloaded from the ‘JGI genome portal’, and RNA-seq data were generated for three coccolithphores E.huxleyi, G.oceanica and I.galbana, under two growth conditions (9mM calcium and 9mM calcium with a spike of sodium carbonate). In order to identify the differential expressed genes, the reads were mapped to the genome and the generated the BAM files were then processed using R-scripts to create the genes count matrices for the three coccolithophore species under the different growth conditions. For E. huxleyi, the number of genes is 3,877 (padj value 0.05) and 2,095 (padj value 0.01). For G. oceanica, the corresponding counts are 3,292 and 1,630.
 The differentially expressed genes shared by E.huxleyi and G.oceanica were compared to the Lipid metabolism proteins present in the E. huxleyi. There were 107 differentially expressed Lipid genes of E.huxleyi and 140 differentially expressed Lipid genes of G.oceanica, of which 57 genes were differentially expressed in both species. Cross-species analysis of Lipid proteins was performed using two types of BLAST queries, blastp and tblastn. Using blastp, 46 Lipid proteins were found to be present in E. huxleyi, G.oceanica and I.galbana, but not Chryosochomulina, tblastn found 36 of such proteins. Out of the 57 differentially expressed Lipid genes in both E.huxleyi and G.oceanica, four were not present in the genome of Chryosochomulina, which suggested that they were likely to be involved in alkenone production of E.huxleyi and G.oceanica, and in need for further studies.

The main aim of this study was to comparatively study the presence and expressions of lipid metabolism proteins in E.huxleyi and three other Prymnesiophyceae species G.oceanica, I.galbana, and Chryosochomulina. The proteins related lipid metabolism of E.huxleyi were downloaded from the ‘JGI genome portal’, and RNA-seq data were generated for three coccolithphores E.huxleyi, G.oceanica and I.galbana, under two growth conditions (9mM calcium and 9mM calcium with a spike of sodium carbonate). In order to identify the differential expressed genes, the reads were mapped to the genome and the generated the BAM files were then processed using R-scripts to create the genes count matrices for the three coccolithophore species under the different growth conditions. For E. huxleyi, the number of genes is 3,877 (padj value 0.05) and 2,095 (padj value 0.01). For G. oceanica, the corresponding counts are 3,292 and 1,630. The differentially expressed genes shared by E.huxleyi and G.oceanica were compared to the Lipid metabolism proteins present in the E. huxleyi. There were 107 differentially expressed Lipid genes of E.huxleyi and 140 differentially expressed Lipid genes of G.oceanica, of which 57 genes were differentially expressed in both species. Cross-species analysis of Lipid proteins was performed using two types of BLAST queries, blastp and tblastn. Using blastp, 46 Lipid proteins were found to be present in E. huxleyi, G.oceanica and I.galbana, but not Chryosochomulina, tblastn found 36 of such proteins. Out of the 57 differentially expressed Lipid genes in both E.huxleyi and G.oceanica, four were not present in the genome of Chryosochomulina, which suggested that they were likely to be involved in alkenone production of E.huxleyi and G.oceanica, and in need for further studies.

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