Over the past decade or so, dramatic developments in our ability to experimentally determine the contents and functions of genomes have taken place. In particular, high-throughput technologies are now inspiring a new understanding of the bacterial genome on a global scale. Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Thus, identification of those genomic elements is prerequisite for understanding the complete regulatory network of a bacterial cell. Here, we measured the frequency of actual members of a heterogeneous transposon mutant pool to determine the contribution of every essential and non-essential element in the E. coli genome under a given growth condition. Also, we applied de novo genome and transcriptome assembly approaches to discover useful gene parts from microalgal species. To enable advanced biofuel research in microalgae we used de novotranscriptome assembly in a non-model microalgae species, Dunaliellatertiolecta which produces large quantities of lipid and starch and subs unique physiological traits advantageous to genomic manipulation. De novotranscriptome assembly and differential expression analysis based upon NGS provides deeper insights into microalgae by metabolic pathway reconstruction without an annotated reference genome sequences.