October 3, 2013  |  Products, procedures + protocols

New Chemistry for PacBio RS II Provides Average 8.5 kb Read Lengths for Complex Genome Studies

Our R&D team has been focusing on chemistry improvements for the PacBio® RS II sequencer and today we are pleased to announce our newest reagent combination, the P5 DNA polymerase with C3 chemistry (P5-C3). Together, they extend our industry-leading sequencing read lengths to an average of approximately 8.5 kb, with the longest reads exceeding 30,000 bases.

The new chemistry includes photo-protected dyes to shield the P5 polymerase from laser-induced damage. With this new protection, the sequencing polymerase is able to generate much longer reads from a single DNA-template molecule. 

Our previously released chemistry, P4-C2, has been successfully used by many customers to completely sequence and assemble bacterial genomes using fast, affordable, and automated pipelines. We anticipate that the longer reads generated by the P5-C3 chemistry will increase the size and complexity of genomes that can be completed in this manner. Both chemistries will continue to be available, and ordering information for the new chemistry is listed below.

Dr. Paul Coupland, a Research Scientist at the Wellcome Trust Sanger Institute, which served as a test site, stated, “With the P5-C3 release, we saw another step change in the evolution of PacBio data. We obtained polymerase mean read lengths of greater than 8,500 bases, enabling us to span longer repeats, phase SNPs, and discover structural variants that were previously hidden. Our first data set was used for hybrid de novo assembly, and when combined with existing P4-C2 data the assembly was considerably improved.”

Kevin Corcoran, our Senior Vice President of Market Development, noted, “Now 50% of the base calls come from reads over 10,000 bases in length, nearly doubling the per-SMRT® Cell throughput. As our customers continue to sequence larger and more complex genomes, the long reads generated from P5-C3 chemistry make it an ideal choice for scaffolding and hybrid de novo assemblies.”

This release also includes 20 kb size-selected library protocols optimized for use with the Sage Science BluePippin™ DNA size selection system, as well as an upgraded version of SMRT Analysis. The latter features a new HGAP 2 assembler that reduces the time required to perform de novo genome assembly and extends the range of genome sizes that can be assembled.

The new part numbers are:
•    DNA Sequencing Reagent 3.0         P/N 100-254-800
•    DNA Sequencing Bundle 3.0 (10 Pack)     P/N 100-259-000
•    DNA/Polymerase Binding Kit P5         P/N 100-256-000
•    Plasmidbell Complex P5 (11 kb)         P/N 100-258-900

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