Transcriptome De novo assembly, clustering, and annotation of novel transcripts

Recent advances in Next Generation Sequencing (NGS) have allowed for unparalleled access to genetic information for organisms in both the functional and phylogenetic realms of biology. Analysis of the RNA transcripts of cells of organisms using Next Generation Sequencing (called RNA-seq) has opened doors for unique insights into the genomic complexity of organisms and has provided researchers with invaluable tools for analysis of function of gene products and phylogenetic relatedness. Application of this method has moved beyond model organisms. It has provided a lot of potentials, in ecological research and comparative transcriptomics, in non-model organisms. This thesis presents an overview on existing applications of RNA-seq in non-model organisms. Furthermore, it presents a new clustering design on handling the data, which led to identification of twelve new fluorescent protein isoforms in corals. In addition, de novo assembly and annotation of the data from polychaete Hermodice carunculata made possible the identification of one new phylogenetic marker and eight bioluminescent protein isoforms. Also, twelve new bilirubin-induced fluorescent proteins were identified from false moray eel Kaupichthys hyproroides. This approach can be applied on any other data.