Delivering a more complete view of genetic diversity
A deeper understanding of the genetics underlying biological traits is a key factor in resolving many agricultural, industrial, and environmental challenges.
The PacBio Systems are suited for a wide range of applications and provide scientists with the ability to:
Explore evolution and diversity in high resolution
Often only a single, fragmented reference genome is available for a species, genus, or even family, limiting discovery potential. Past use of short, biased next-generation reads often resulted in poor draft-quality genomes. High-quality reference genomes with evidence-based gene annotations deliver the most complete view of genetic diversity, allowing scientists to make novel and meaningful discoveries.
Uncover key genes for improved agricultural products
Whether breeding crops or livestock, preventing and treating disease, or protecting against pests, a deeper understanding of genetic components is critical for designing high-performance products. High-throughput, long-read, and cost-effective sequencing produces the most complete and accurate view of genes of interest, enabling a faster response to market demands.
Engineer organisms with precision for industrial applications
By optimizing existing biochemical pathways or engineering new ones, scientists turn microbes and plants into safe, contained manufacturing centers. SMRT Sequencing delivers a seamless process for sequencing individual organisms or parsing out microbial communities, resulting in complete and accurate genome assemblies as a basis for engineering.
SMRT Sequencing Project Calculators
Tell us about your plant or animal genome of interest and receive an estimate on the time and materials needed using the Sequel System for:
- Whole genome sequencing for de novo assembly
- Iso-Seq method for full-length transcript isoforms
Spotlight: Closing Gaps, Advancing Science
A new article in Science highlights how PacBio sequencing is improving plant and animal genomes. Explore this research further.
Pennisi, E., 2017. New technologies boost genome quality. Science. Jul 7;357(6346):10-11.
Selected Resources
- Koren, Sergey et al. (2018) De novo assembly of haplotype-resolved genomes with trio binning. Nature biotechnology
- Wang, Dan et al. (2018) Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nature biotechnology
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Hoff, Siv Nam Khang et al. (2018) Long-read sequence capture of the hemoglobin gene clusters across gadid species. Molecular ecology resources
- Gupta, Ishaan et al. (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nature biotechnology
- Dougherty, Max L et al. (2018) Transcriptional fates of human-specific segmental duplications in brain. Genome research
- Tran, Hue T M et al. (2018) Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant biotechnology journal
- Bull, Simon E et al. (2018) Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch. Science advances
- Gong, Gaorui et al. (2018) Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. GigaScience
- Sun, Silong et al. (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature genetics
- Nudelman, German et al. (2018) High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome research
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Sutton, Jolene et al. (2018) A high-quality, long-read de novo genome assembly to aid conservation of Hawaii’s last remaining crow species Genes
- VanBuren, Robert et al. (2018) A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience
- Li, Yao et al. (2018) A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing. DNA research
- Redondo, Miguel A et al. (2018) Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits. The ISME journal
- Löber, Ulrike et al. (2018) Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America
- Zhou, Chao et al. (2018) Identification and analysis of adenine N6-methylation sites in the rice genome. Nature plants
- Heeger, Felix et al. (2018) Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Molecular ecology resources
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Roach, Michael J. et al. (2018) Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay BioRxiv
- Breaux, Breanna et al. (2018) The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. Developmental and comparative immunology
- Zhu, Chunhui et al. (2018) Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection. Gene
- Poulter, Russell T. M. et al. (2018) Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic. Scientific reports
- Johnson, Rebecca N et al. (2018) Adaptation and conservation insights from the koala genome. Nature genetics
- Li, Fay-Wei et al. (2018) Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature plants
- Gao, Fei et al. (2018) Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. GigaScience
- Marx, Vivien et al. (2018) What makes birds and bats the talk of the town. Nature methods
- Zuo, Chunman et al. (2018) Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnology for biofuels
- Wang, Bo et al. (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome research
- Shields, Emily J et al. (2018) High-quality genome assemblies reveal long non-coding RNAs expressed in ant brains. Cell reports
- Kronenberg, Zev N et al. (2018) High-resolution comparative analysis of great ape genomes. Science
- Du, Xiongming et al. (2018) Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature genetics
- Raymond, Olivier et al. (2018) The Rosa genome provides new insights into the domestication of modern roses. Nature genetics
- Zhang, Hangxiao et al. (2018) Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. BMC plant biology
- Poster: Blethrow, J. Sisneros, N. et al. (2018) Best practices for whole genome sequencing using the Sequel System
- Poster: Vierra, Michelle et al. (2018) Full-length transcript profiling with the Iso-Seq method for improved genome annotations
- Poster: Korlach, Jonas et al. (2018) High-quality de novo genome assembly and intra-individual mitochondrial instability in the critically endangered kakapo
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Kingan, S., et al. (2018) Best practices for diploid assembly of complex genomes using PacBio: A case study of Cascade Hops
- Poster: Vierra, Michelle et al. (2018) Characterizing the pan-genome of maize with PacBio SMRT Sequencing
- Poster: Concepion, C., et al. (2018) De novo assembly and preliminary annotation of the Schizocardium californicum genome
- Poster: Tseng, E., et al. (2018) Haplotyping of full-length transcript reads from long-read sequencing can reveal allelic imbalances in isoform expression
- Poster: Concepcion, G., et al. (2018) Structural variant detection in crops using PacBio SMRT Sequencing
- Poster: Vierra, M. et al. (2017) From RNA to full-length transcripts: The PacBio Iso-Seq method for transcriptome analysis and genome annotation
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Korlach, Jonas et al. (2017) De novo PacBio long-read assembled avian genomes correct and add to genes important in neuroscience and conservation research
- Poster: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Warr, A. et al. (2017) High-quality, highly contiguous re-assembly of the pig genome
- Poster: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Poster: Heiner, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- Poster: Clark, T et al. (2017) Full-length cDNA sequencing on the PacBio Sequel platform
- Poster: Roach, M. et al. (2016) Assessing diversity and clonal variation of Australia’s grapevine germplasm: Curating the FALCON-Unzip Chardonnay de novo genome assembly
- Poster: Tseng, Elizabeth et al. (2016) Reconstruction of the spinach coding genome using full-length transcriptome without a reference genome
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Chin, Jason et al. (2016) Un-zipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies
- Presentation: Chin, Jason et al. (2016) Diploid genome assembly and comprehensive haplotype sequence reconstruction
- Poster: Clark, Tyson et al. (2016) Full-length cDNA sequencing for genome annotation and analysis of alternative splicing
- Poster: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Hall, Richard J et al. (2016) Profiling metagenomic communities using circular consensus and Single Molecule, Real-Time Sequencing
- Poster: Muehling, Jill R et al. (2016) SMRT Sequencing of the alala genome
- Poster: Lee, Hayan et al. (2015) The resurgence of reference quality genome
- Poster: Rank, David et al. (2015) Best practices for whole-genome de novo sequencing with long-read SMRT Sequencing.
- Presentation: Schatz, Michael et al. (2015) The resurgence of reference quality genome sequence.
- Presentation: VanBuren, Robert et al. (2015) De novo assembly of a complex panicoid grass genome using ultra-long PacBio reads with P6C4 chemistry
- Presentation: Strickler, Susan R et al. (2015) Genome assembly strategies of the recent polyploid, Coffea arabica.
- Presentation: Wing, Rod A et al. (2015) Old school/new school genome sequencing: One step backward — a quantum leap forward.
- Smith, Tim (2018) User Group Meeting: Application of genome assembly in Bovinae species
- Korlach, Jonas (2018) User Group Meeting: Low-input workflow for PacBio de novo genome assemblies
- Pillai, Nisha (2018) Webinar: Survey of transcriptome diversity using Iso-Seq analysis
- (2018) Educational Video: Step 1 – from sample to sequencing data for de novo assembly
- (2018) Educational Video: Step 2 – de novo assembly of a genome
- Pillai, Nisha (2018) Webinar: A sketch of assembly recipes for PacBio data
- Kuo, Richard (2018) Webinar: Using Iso-Seq analysis to build a better annotation
- Ballard, Bill (2018) PAG Conference: Domestication: through the canines of a dingo
- Renner, Tanya (2018) PAG Conference: Long-read sequencing reveals complex genomic architecture in independent carnivorous plant lineages
- Williams, John (2018) PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through Iso-seq analysis
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- Kujawa, Steve (2017) Webinar: PacBio Targeted Sequencing of Long Amplicons Using PCR or Hybrid Capture
- Turner, Stephen (2017) Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries
- Neafsey, Daniel (2017) AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector
- Roy, Margaret (2017) AGBT PacBio Workshop: De novo sequencing of the naked mole rat genome
- Sedlazeck, Fritz (2017) AGBT Virtual Poster: Quantifying the impact of improved genome assemblies on functional genomics
- Simon, Matt (2017) Video: Get ready for super coffee strains. Scientists just sequenced the plant’s DNA
- (2017) Tutorial: Iso-Seq analysis application [SMRT Link v5.0.0]
- (2017) Tutorial: Long amplicon analysis application [SMRT Link v5.0.0]
- Jarvis, Erich (2017) PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies
- Johnson, Rebecca (2017) PAG PacBio Workshop: De novo sequencing of the koala genome
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Wing, Rod (2017) PAG PacBio Workshop: Introducing 5 new high-quality PacBio genome assemblies for rice to help solve the 10-billion people question
- Korlach, Jonas (2017) PAG PacBio Workshop: SMRT Sequencing for complete genomes
- Kuo, Richard (2017) PAG PacBio Workshop: Using the Iso-Seq method to fill in your a_no__tion
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Hannigan, Brett (2016) DNAnexus Webinar: Simplifying de novo assembly with PacBio tools available on DNAnexus: FALCON
- Hill, Christopher (2016) AGBT Conference: Long-read sequence of the gorilla genome
- Ranade, Swati (2016) AGBT Virtual Poster: Immune regions are no longer incomprehensible with SMRT Sequencing
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Heiner, Cheryl (2016) AGBT Virtual Poster: Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Heiner, Cheryl (2016) AGBT Virtual Poster: Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Chin, Jason (2016) AGBT Virtual Poster: Unzipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive haplotig assemblies
- Ware, Doreen (2016) PAG PacBio Workshop: A-maize-ing time for plant science – SMRT Sequencing of the maize genome and transcriptome
- Ryder, Oliver (2016) PAG PacBio Workshop: Conservation genomics of a critically endangered Hawaiian bird: A high quality genome assembly of the ‘alala will assist in population management and reintroduction
- PacBio Certified Service Providers (2018)
- Application Brief: Large genome whole genome sequencing – Best Practices (2018)
- Application Brief: Targeted Sequencing of Amplicons – Best Practices (2018)
- Application Brief: Long-read RNA sequencing – Best Practices (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Infographic: Gold-standard reference genomes accelerate science (2018)
- De Novo Assembly Brochure: Assembly options for your SMRT Sequencing data (2018)
- Technical Note: Preparing libraries for PacBio whole genome sequencing for de novo assembly – Quality control and size selection (2018)
- Technical Note: Preparing DNA for PacBio whole genome sequencing for de novo assembly – Quality control and shearing (2018)
- Technical Note: Preparing samples for PacBio whole genome sequencing for de novo assembly – Collection and storage (2018)
- Case Study: Pioneering a pan-genome reference collection (2018)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center. (2017)
- Case Study: PacBio and Dovetail – For cashew genome, combining technologies yields chromosome-scale assembly. (2017)
- Case Study: Breeding a better Cabernet – SMRT Sequencing provides detailed view of grape genome. (2016)
- Application Note: Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies (2016)
- Case Study: First comprehensive view of maize genome reveals regulatory and structural mechanisms (2016)