Focus in, discover more
Accurately map microbial variation by focusing on specific regions of the genome while maintaining complete and uniform coverage.
Confident identifications with a complete view of variation
Polymorphisms can take the form of structural variation within a genome or its mobile elements, and must be clearly defined for the most confident and accurate conclusions. Single Molecule, Real-Time (SMRT) Sequencing provides the read length needed to clearly resolve structural variants within specific regions of interest in their genomic context. Additionally, SMRT Sequencing allows for the identification of individual members of complex microbial populations — including 16S rRNA species-level identification — and the resolution of complete plasmids or viral quasispecies.
This technology advances your microbial and viral research through the ability to:
- Resolve complex populations in viral or metagenomic samples
- Map order and orientation of multiply-inserted phage elements
- Target regions in host organisms to study viral integration and integration sites
- Phase variations across targeted regions
- Perform multiplexed multi-locus sequence typing (MLST)
Workflow: from targeted region to accurate variant or haplotype
- Library preparation
- SMRT Sequencing with PacBio Systems
- Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
- Achieve ~10 kb average read lengths, with some reads as long as 60 kb
- Adjust run times (0.5 to 6 hours) to maximize sample throughput and turn-around time
- Obtain consensus accuracies > 99.999% by avoiding mapping and systematic errors
- Produce high single-molecule consensus accuracies through multiple observations of single circularized templates for complex population resolution
- Data analysis with SMRT Analysis or PacBio DevNet
- Long Amplicon Analysis (LAA) for reference-free generation of de novo haplotype sequences from pooled amplicons
- Minor Variant Analysis for detection and quantitation of single nucleotide polymorphisms
- ClusterConsensus for reference-free deconvolution of genomes in a complex mixture
- HGAP for comprehensive de novo assembly of BACs or fosmids
Spotlight: Long reads elucidate HIV envelope variants susceptible to antibody targeting
Caskey and coworkers used targeted SMRT Sequencing to determine that pre-existing variants in the HIV envelope may confer resistance to antibodies. Explore this research further:
Caskey, M. et al., 2017. Antibody 10-1074 suppresses viremia in HIV-1-infected individuals. Nature Medicine, ePub Ahead of Print.
To learn more about obtaining a complete view of microbial variation, contact us.
- Haig, Sarah-Jane et al. (2018) A high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and Mycobacterium avium. mBio
- Verhey, Theodore B et al. (2017) Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline. Molecular Microbiology
- Fraiture, Marie-Alice et al. (2017) An integrated strategy combining DNA walking and NGS to detect GMOs. Food Chemistry
- Dara, Antoine et al. (2017) A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples. Malaria Journal
- Borràs, Daniel M et al. (2017) Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Human Mutation
- Fischer, Matthias G et al. (2016) Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature
- Eudes, Aymerick et al. (2016) Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microbial Cell Factories
- Oren, Matan et al. (2016) Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family. BMC Genomics
- Witek, Kamil et al. (2016) Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nature Biotechnology
- Sheppard, Anna E et al. (2016) Nested Russian doll-like genetic mobility drives rapid dissemination of the Carbapenem resistance gene blaKPC Antimicrobial Agents and Chemotherapy
- Badran, Ahmed H et al. (2016) Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature
- Witek, Kamil et al. (2016) SMRT RenSeq protocol Protocol Exchange
- Zhang, Huibin et al. (2016) Comprehensive mutagenesis of the fimS promoter regulatory switch reveals novel regulation of type 1 pili in uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America
- Hall, Andrew Brantley et al. (2016) Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences of the United States of America
- De Ravin, Suk See et al. (2016) Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nature Biotechnology
- Hüser, Daniela et al. (2014) Adeno-associated virus type 2 wild-type and vector-mediated genomic integration profiles of human diploid fibroblasts analyzed by third-generation PacBio DNA sequencing. Journal of Virology
- Lu, Shuguang et al. (2014) Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity. BMC Genomics
- Huddleston, John et al. (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research
- Roberts, Richard J et al. (2013) The advantages of SMRT sequencing. Genome Biology
- Chin, Chen-Shan et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods
- Oldfield, Lauren M et al. (2017) Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods. Proceedings of the National Academy of Sciences of the United States of America
- Ma, Fang-Fang et al. (2017) Molecular characterization of NBS-LRR genes in the soybean Rsv3 locus reveals several divergent alleles that likely confer resistance to the soybean mosaic virus. Theoretical and Applied Genetics.
- Ba Abdullah, Mohammed et al. (2017) Heterogeneity of the Epstein-Barr virus major internal repeat reveals evolutionary mechanisms of EBV and a functional defect in the prototype EBV strain B95-8. Journal of Virology
- Amlinger, Lina et al. (2017) Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Scientific Reports
- Matrosova, Vera Y et al. (2017) High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Standards in Genomic Sciences
- Li, Ruichao et al. (2017) Evolution and comparative genomics of pAQU-like conjugative plasmids in Vibrio species. The Journal of Antimicrobial Chemotherapy
- Bratulic, Sinisa et al. (2017) Mistranslation can enhance fitness through purging of deleterious mutations. Nature Communications
- Hoopes, James I et al. (2017) Avoidance of APOBEC3B-induced mutation by error-free lesion bypass. Nucleic Acids Research
- Novikova, Polina Yu et al. (2017) Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Molecular Biology and Evolution
- Quan, Jingjing et al. (2017) Prevalence of mcr-1 in Escherichia coli and Klebsiella pneumoniae recovered from bloodstream infections in China: a multicentre longitudinal study. The Lancet. Infectious Diseases
- Bento, Gilberto et al. (2017) The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model. PLoS Genetics
- Bennett, Henrietta W et al. (2016) TeloPCR-seq: a high-throughput sequencing approach for telomeres. FEBS Letters
- Chen, Yuan et al. (2016) Efficient, cost-effective, high-throughput, Multilocus Sequencing Typing (MLST) method, NGMLST, and the analytical software program MLSTEZ. Methods in Molecular Biology
- Wong, Marcus H et al. (2016) Complete sequence of a F33:A-:B- conjugative plasmid carrying the oqxAB, fosA3, and blaCTX-M-55 elements from a foodborne Escherichia coli strain. Frontiers in Microbiology
- Feasey, Nicholas A et al. (2016) Distinct Salmonella enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nature Genetics
- Poster: Pollard, M. O. et al. (2016) The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Lee, Walter et al. (2015) Barcoding strategies for multiplexing of samples using a long-read sequencing technology.
- Poster: Brown, Michael et al. (2015) High-accuracy, single-base resolution of near-full-length HIV genomes.
- Poster: Murrell, Ben et al. (2015) Full-length env deep sequencing in a donor with broadly neutralizing V1/V2 antibodies.
- Poster: Brown, Michael et al. (2015) Sequencing complex mixtures of HIV-1 genomes with single-base resolution.
- Presentation: Alexander, David et al. (2015) PacBio SMRT Analysis 3.0 preview
- Poster: Clark, Tyson et al. (2015) Complete microbial genomes, epigenomes, and transcriptomes using long-read PacBio Sequencing.
- Turner, Stephen (2017) Webinar: An Introduction to PacBio’s Long-Read Sequencing & How It Has Been Used to Make Important Scientific Discoveries
- Morey, Robert (2016) AGBT Virtual Poster: Using PacBio sequencing as a synthetic biology error analysis tool
- Morey, Robert (2016) Customer Experience: Synthetic Genomics using SMRT Sequencing for efficient and cost-effective development of long, synthetic DNA contructs
- Sebra, Robert (2015) Customer Experience: At Mount Sinai School of Medicine, sequence reads longer than 70 kb
- Industrial Biotechnology Brochure: Fuel biotech discovery with confident characterization of microbes and their communities. (2016)
- Targeted Sequencing Application Brochure: Capture your regions of interest in high resolution. (2015)
- Microbiology and Infectious Disease Brochure: Novel insights into microbial and viral complexity. (2015)