Computational approaches for in-depth analysis of cDNA sequence tags

Abstract: Major recent improvements in biotechnology have led to an accelerated production of DNA sequences. The completion of the human genome sequence, along with the genomes of more than two hundred other species, has marked the arrival of the genome era. The ultimate goal is to understand the structure and function of genomes and their genes. This thesis has focused on the computational analysis of complementary DNA (cDNA) sequences. These are copies of mRNA transcripts that correspond to the coding regions of genomes.Studying the expression patterns of genes is essential for understanding gene function. Many gene expression profiling techniques generate short sequence tags that derive from transcripts. A pilot study was performed to assess the feasibility of using the pyrosequencing platform for gene expression analysis. The sequences generated by pyrosequencing in most cases (? 85%) were long enough (> 18 nucleotides) to uniquely identify the corresponding transcripts through database searches. Aspects of transcript identification by short sequence tags were further investigated in a number of public databases, revealing that a tag length 16-17 nucleotides was sufficient for unique identifi- cation.Longer transcript representations are obtained from expressed sequence tag (EST) sequencing. Method development for the analysis and maintenance of large EST data sets has been performed on data from poplar, which is a tree of commercial interest to the forest biotechnology industry. In 2003 a large ESTsequencing project reached > 100 000 reads, providing a unique resource for tree biology research. ESTs have been grouped into clusters and singletons that represent potential genes. Preliminary analyses have estimated gene content in Populus to be very similar to that of model organism Arabidopsis thaliana.EST data collections provide a rich source for mining polymorphisms. A software application was developed and applied to EST data from two Populus species, and candidate single nucleotide polymorphisms (SNPs) were recorded. A study of genetic variation between the species revealed a striking similarity, with orthologous pairs being > 98% identical on the protein level.Keywords: cDNA, EST, gene expression, SNP, SAGE, polymorphism, assembly, clustering, DNA sequencing, pyrosequencing, mRNA transcript, orthology, tree biotechnology, restriction enzyme