Wednesday, June 29, 2011

Something old, something new: Nextera and CopyControl technologies

With the advent of next-generation sequencing techniques, genomic cloning has taken on a new role in de novo and reference-genome sequencing. Previously, Kitzman et al.1 generated massive amounts of shotgun sequence data from a human library by sequencing 120 pools of CopyControl™ fosmid clones using Nextera™ DNA library preparation technology. This method generated sequencing data of sufficient depth to assemble a complete haplotype-resolved genome for the individual being studied.

However, a recent study by Naka et al.2 used a combination of direct genomic next-generation sequencing and CopyControl fosmid cloning to generate and confirm the de novo sequence of the bacterium Vibrio anguillarum strain 775. While deep sequencing generated 32X coverage of the bacterial genome, there were gaps in the sequence data that required confirmation, or contig “gap-filling.” The CopyControl fosmid library allowed the generation of sequence data confirming not only the taxonomy of the new organism, but also demonstrating the synergistic approach of using deep sequencing techniques together with classical Sanger-based sequencing.

ResearchBlogging.org1. Kitzman, J. et al. (2010). Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology, 29 (1), 59-63 DOI: 10.1038/nbt.1740
2. Naka, H. et al. (2011). Complete Genome Sequence of the Marine Fish Pathogen Vibrio anguillarum Harboring the pJM1 Virulence Plasmid and Genomic Comparison with Other Virulent Strains of V. anguillarum and V. ordalii Infection and Immunity, 79 (7), 2889-2900 DOI: 10.1128/IAI.05138-11

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