SYSTEMATIC SEQUENCING OF COMPLEX GENOMES

Biology and medicine are in the midst of a revolution, the full extent of which will probably not be realized for many years to come. The catalyst for this revolution is the Human Genome Project1 and related activities that aim to develop improved technologies for analysing DNA, to generate detailed information about the genomes of numerous organisms, and to establish powerful experimental and computational approaches for studying genome structure and function. The past few years have seen a remarkable crescendo in accomplishments related to DNA sequencing, with genome sequences being generated for several key experimental organisms, including a yeast (Saccharomyces cerevisiae), a nematode (Caenorhabditis elegans), a fly (Drosophila melanogaster), a plant (Arabidopsis thaliana) and the human (Homo sapiens). Collectively, the generation of these sequence data and others is launching the ‘sequence-based era’of biomedical research. Associated with the above accomplishments has been the refinement of existing strategies for genome sequencing, as well as the development of new ones. Among these are approaches that make extensive use of large-insert clones and associated physical maps, some that take a whole-genome approach without using clone-based physical maps, and others that use a hybrid strategy that involves elements of the other two. Each of these general strategies for genome sequencing is described in this review. There are many potential uses of genome-sequence data. In some cases, a detailed and accurate sequencebased ‘blueprint’ of a genome is required (for example, to establish a comprehensive gene catalogue and/or to gain insight into long-range genome organization), whereas in other cases, an incomplete survey will suffice (for example, to acquire information about the repetitive sequences in a genome and/or to carry out simple, non-comprehensive comparisons to sequences from other organisms). Importantly, the intended use(s) of genome-sequence data must be carefully considered when choosing a specific sequencing strategy and defining the end point of a particular project. These issues, as well as the plans for future sequencing initiatives by the Human Genome Project, are also discussed.

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