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Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation
 
Paul Coupland1, Tamir Chandra2, Mike Quail1, Wolf Reik2, and Harold Swerdlow1
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Supplementary Material

Finally, the technique was used to sequence linear molecules of Candidatus Phytoplasma mali, a plant-pathogenic mycoplasma with a small genome of ∼600 kb that is 21.4% GC and characterized by large terminal inverted repeats and covalently closed hairpin ends (20). The DNA was sheared to approximately 3-kb fragments and a 25-ng aliquot was sequenced using random hexamers in a similar manner to that described previously. From a single SMRT cell with 2 × 45 min movies, only 870 post-filter reads were generated of which 63 reads mapped, with a mean consensus accuracy of 84.4%. The mean mapped read-length was 817 bp and the coverage only 0.08%. The poor mapping rate is most likely due to a greater percentage of low-quality reads from this particular sample. Although the yield is poor, direct sequencing of these linear DNA molecules shows some promise too. A blastn (21) search using the NCBI server against the refseq_genomic database called out Candidatus Phytoplasma mali as the most likely taxonomic hit (Supplementary Table 1). This suggests it is possible to obtain enough information from very few mapped reads to begin to identify the genomes present in a sample. However, comparing the difference in data yield between the S. aureus and Ca. Phytoplasma mali, it is clear that further optimization of the method is required to improve the number of reads that can be mapped when sequencing linear molecules from a variety of genomic samples.

The method described here utilizes the PacBio RS platform for direct sequencing, enabling the generation of sequence data from small single- and double-stranded DNA genomes. Potentially this technique also could be applied to circularized molecules, e.g., amplicons or sheared fragments that have been circularized. However, the additional circularization step and clean up would mean relatively minor time and DNA savings compared with current PacBio protocols. The direct sequencing technique could allow the identification of plasmids present in a bacterial sample in an extremely straightforward and fast manner. Although there is an indication that different genomes may be more or less accessible with this method, we have demonstrated its application to sequencing ssDNA and dsDNA viruses, plasmid vector models for methylation studies, antibiotic resistance gene-carrying plasmids, and the entire genome of a clinically relevant microbial pathogen. All of these were performed without the need for library preparation, and it is possible to generate sequence data within 8 h from <1 ng of DNA without a PCR amplification step. The fact that our method can be performed without a priori knowledge of any sequence and with no organism-specific reagents, coupled with its simplicity and speed, makes it particularly well suited for use in acute disease and infectious outbreak scenarios.

Acknowledgments

We would like to thank NEB for providing the M13 primers which were not currently available for purchase. Sascha Sauer of the Max-Planck-Institute for Molecular Genetics for isolating and providing the Candidatus Phytoplasma mali sample. Theresa Feltwell of The Wellcome Trust Sanger Institute for culturing S. aureus TW20 and performing the plasmid prep. Albert Jeltsch and Tomasz Jurkowski for providing the original Dam constructs. This work was supported by the Wellcome Trust grant 098051 (PC, MQ, HS) and The Cambridge Cancer Center (TC, WR). ESGI – The research leading to these results has received funding from the Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 262055.

Competing interests

The authors declare no competing interests.

Correspondence
Address correspondence to Paul Coupland, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK. Email: [email protected]

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