Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

摘要: Extensive computational and database tools are available to mine genomic genetic databases for model organisms, but little data is many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques powerful, particularly detecting sequences present in copies per genome. However these methods time-consuming have potential drawbacks. High throughput 454 provides an alternative method by which much information can be gained quickly cheaply from high-coverage DNA. We sequenced 78 million base-pairs randomly sheared soybean DNA passed our quality criteria. Computational analysis the survey provided global on abundant repetitive soybean. The sequence was used determine copy number across regions clones contigs discover higher-order structures within satellite repeats. created annotated, online multiple low bias pyrosequencing against repeat demonstrated overall composition data, matches well past estimates content obtained re-association kinetics (Cot analysis). This approach a aid shotgun genome assembly, allowing rapid assessment any clone clone-end sequence. In addition, we show that partial provide access protein-coding sequences.