Shotgun sequencing, clone pooling, and comparative strategies for mapping and sequencing

Comparative genomic sequencing and analysis offers new wealth of information for target selection and the development of therapeutics. This article focuses on the following two key innovations in mapping and sequencing: first, shotgun sequencing of clone pools to combine the benefits of whole-genome shotgun and clone-by-clone strategies, and second, the leveraging of newly available assembled genomic sequences to improve the effectiveness of new sequencing projects through comparative mapping and comparative sequence assembly. The following specific sequencing and mapping methods are discussed in detail: clone-array pooled shotgun sequencing (CAPSS); transversal shotgun pooling designs; clone-array pooled shotgun mapping (CAPS-MAP); pooled genomic indexing (PGI); short-tag pooled genomic indexing (ST-PGI); and comparative sequence assembly (the CSA™ method). The methods can be implemented with only modest modifications of current large-scale sequencing pipelines and are highly synergistic with the next generation of sequencing technologies.