Sequence plants and animals with confidence
Large and complex genomes present unique challenges such as polyploidy and high levels of heterozygosity. PacBio offers the long reads with high accuracy necessary to overcome these challenges.
Insect Biology
Insect Biology Develop disease prevention methods, understand basic biology, and improve pest control using a population or a single individual.
Genome from a single mosquito | Low DNA input workflow | Corn leaf aphid genome
Crop Improvements
Crop ImprovementsUncover new biology to improve crop health, conduct trait selection, and enhance breeding efficiency.
Garlic transcriptome study | Autopolyploid sugarcane genome | Structural variants in grapevine | Mining plant genomes
Animal Health and Breeding
Animal Health and BreedingInvestigate animal genetics to study patterns of inheritance, immunology, and domestication in high resolution.
Phased diploid genome assembly | Canine domestication genes | MHC in primates
Marine Biodiversity
Marine BiodiversityDive into the depths of marine ecosystems to study evolution, reveal insights into developmental and address the challenges of climate change.
Clown fish genome | Coral microbiome characterization | Hemoglobin gene clusters in codfish
Conservation
ConservationExamine the genetic diversity of species-at-risk to support assisted reproduction, wildlife management, and sustainability.
Bluefin tuna genomes | Turtle dove population decline | 25 genomes effort for conservation
 | Whole Genome Sequencing Produce reference-quality genomes with phased haplotypes from even small-bodied organisms |
 | Structural Variant Calling Use high-sensitivity variant calls with low false discovery rate to gain actionable insights across populations |
 | Targeted Sequencing Choose from flexible options to target regions to access to all variants even in the most complex regions |
 | RNA Sequencing Access full-length transcript sequences to identify novel genes and transcripts and improve genome annotation |
Selected Resources
- Kingan, Sarah B et al. (2019) A High-Quality Genome Assembly from a Single, Field collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System bioRxiv
- Watson, Corey T. et al. (2019) Germline murine immunoglobulin IGHV genes in wild-derived and classical inbred strains: a comparison bioRxiv
- Chang, Ching-Ho et al. (2019) Islands of retroelements are major components of Drosophila centromeres PLOS Biology
- Zhuang, Weijian et al. (2019) The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature genetics
- Kronenberg, Zev N. et al. (2019) Extended haplotype phasing of de novo genome assemblies with FALCON-Phase bioRxiv
- Zhang, Xiujuan et al. (2019) Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Fish & shellfish immunology
- Zhao, Dongyan et al. (2019) A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. GigaScience
- Qiao, Dahe et al. (2019) Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis). Scientific reports
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Low, Wai Yee et al. (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature communications
- Ruan, Jue et al. (2019) Fast and accurate long-read assembly with wtdbg2 bioRxiv
- Wenger, Aaron M et al. (2019) Highly-accurate long-read sequencing improves variant detection and assembly of a human genome bioRxiv
- Formenti, Giulio et al. (2019) SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). GigaScience
- Bell, Zachary W et al. (2019) Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Scientific reports
- Beaulaurier, John et al. (2018) Deciphering bacterial epigenomes using modern sequencing technologies Nature reviews. Genetics
- Editorial et al. (2018) A reference standard for genome biology Nature biotechnology
- Bruijnesteijn, Jesse et al. (2018) Extensive alternative splicing of KIR transcripts. Frontiers in immunology
- Wittmeyer, Kameron et al. (2018) The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon. The Plant cell
- Matthews, Benjamin J et al. (2018) Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature
- Laverty, Kaitlin U et al. (2018) A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the THC/CBD acid synthase locus. Genome research
- Chao, Yuehui et al. (2018) Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing. BMC plant biology
- Gong, Gaorui et al. (2018) Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. GigaScience
- Roach, Michael J et al. (2018) Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS genetics
- Kim, Bo-Mi et al. (2018) The genome of common long-arm octopus Octopus minor. GigaScience
- Koren, Sergey et al. (2018) De novo assembly of haplotype-resolved genomes with trio binning. Nature biotechnology
- Mehta, Devang et al. (2018) A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic acids research
- Zhang, Jisen et al. (2018) Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature genetics
- Wang, Dan et al. (2018) Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nature biotechnology
- Wen, Ming et al. (2018) Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing. GigaScience
- Grech-Baran, Marta et al. (2018) Extreme resistance to Potato Virus Y in potato carrying the Rysto gene is mediated by a TIR-NLR immune receptor BioRxiv
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Chen, Wenbo et al. (2018) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch) BioRxiv
- 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
- Poster: Vierra, M. et al. (2019) Structural variant detection in crops using low-fold coverage long-read sequencing
- Poster: Duncan, Turner et al. (2019) A low DNA input protocol for high-quality PacBio de novo genome assemblies
- Poster: Ekholm, Jenny et al. (2019) Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results
- Poster: Kingan, Sarah B. et al. (2019) A low DNA input protocol for high-quality PacBio de novo genome assemblies from single invertebrate individuals
- Poster: Tseng, Elizabeth et al. (2019) Haplotyping using full-length transcript sequencing reveals allele-specific expression
- Poster: Vierra, Michelle et al. (2019) Library prep and bioinformatics improvements for full-length transcript sequencing on the PacBio Sequel System
- Poster: Peluso, Paul et al. (2019) Single molecule high-fidelity (HiFi) Sequencing with >10 kb libraries
- 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
- Korlach, Jonas and Garimella, Kiran and Tallon, Luke and McCarthy, Shane (2019) Webinar: Sequence with Confidence – Introducing the Sequel II System
- Hunkapiller, Michael (2019) AGBT Presentation: HiFi long reads for comprehensive genomic analysis
- Underwood, Jason (2019) AGBT Presentation: Single cell isoform sequencing (scIso-Seq) identifies novel full-length mRNAs and cell type-specific expression
- Badgett, Marty (2019) AGBT Presentation: The Sequel II System – the next evolution of SMRT Sequencing
- Fengler, Kevin (2019) PAG Conference: Dawn of the crop pangenome era
- Blethrow, Justin (2019) PAG Conference: How SMRT Sequencing is accelerating plant and animal genomics
- Tseng, Elizabeth (2019) PAG Conference: Iso-Seq analysis for plant & animal genomes – annotation evaluation & phasing
- Clark, Andrew (2019) PAG Conference: Reference-quality drosophila genome assemblies for evolutionary analysis of previously inaccessible genomic regions
- Vernes, Sonia (2019) PAG Conference: The Bat1K project: bat genome, biology and implications
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- (2018) Tutorial: Iso-Seq analysis application [SMRT Link v6.0.0]
- Block, Barbara and Peluso, Paul (2018) Webinar: Assembling high-quality genomes to solve nature’s mysteries
- 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: Assessing the targeted regions using a PacBio Amplicon analysis applications
- 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: 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
- Technical Note: Preparing DNA for PacBio whole genome sequencing for de novo assembly – Quality control and shearing (2019)
- Technical Note: Preparing libraries for PacBio whole genome sequencing for de novo assembly – Quality control and size selection (2019)
- PacBio Certified Service Providers (2019)
- Application Brief: Structural variant detection using whole genome sequencing – Best Practices (2019)
- Application Brief: Whole genome sequencing for de novo assembly – Best Practices (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Note: Low DNA input workflow considerations for de novo genome assembly (2019)
- Product Note: SMRTbell express template prep 2.0 for large-insert libraries (2019)
- Application Brief: Targeted sequencing for amplicons – Best Practices (2018)
- Application Brief: Long-read RNA sequencing – Best Practices (2018)
- Infographic: Gold-standard reference genomes accelerate science (2018)
- De Novo Assembly Brochure: Assembly options for your SMRT Sequencing data (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)