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An Examination Of Targeted Gene Neighborhoods In Strawberry, Thomas M. Davis, Melanie E. Shields, Qian Zhang, Denise Tombolato-Terzić, Jeffrey L. Bennetzen, Ana C. Pontaroli, Hao Wang, Qin Yao, Phillip Sanmiguel, Kevin M. Folta

Biological Sciences

This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.

An Enhanced Method For Sequence Walking And Paralog Mining: Topo® Vector-Ligation Pcr, Benjamin B. Orcheski, Thomas M. Davis

Biological Sciences

Background

Although technological advances allow for the economical acquisition of whole genome sequences, many organisms' genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO^® Vector-Ligation PCR (or TVL-PCR) that innovatively …