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
- Ye, Jiabao et al. (2019) A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis Industrial Crops and Products
- Zhou, Yongfeng et al. (2019) The population genetics of structural variants in grapevine domestication. Nature plants
- Wenger, Aaron M et al. (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature biotechnology
- Watson, Corey T et al. (2019) A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunology and cell biology
- Van de Weyer, Anna-Lena et al. (2019) A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell
- Bickhart, Derek M et al. (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology
- Jaworski, Coline C et al. (2019) Chromosome-level hybrid de novo genome assemblies as an attainable option for non-model organisms BioRxiv
- Low, Wai Yee et al. (2019) Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation bioRxiv
- Loit, Kaire et al. (2019) Relative Performance of MinION (Oxford Nanopore Technologies) vs. Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Applied and environmental microbiology
- Martijn, Joran et al. (2019) Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environmental microbiology
- Novák, Karel et al. (2019) Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing Archives Animal Breeding
- McCartney, Michael A. et al. (2019) The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research BioRxiv
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Warr, Amanda et al. (2019) An improved pig reference genome sequence to enable pig genetics and genomics research BioRxiv
- Chen, Zelin et al. (2019) De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Science advances
- Yang, Ning et al. (2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nature genetics
- Sánchez-Pérez, R et al. (2019) Mutation of a bHLH transcription factor allowed almond domestication. Science
- Yoshimura, Jun et al. (2019) Recompleting the Caenorhabditis elegans genome. Genome research
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- Wang, Bo et al. (2019) Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize BioRxiv
- 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
- Zhang, Peng et al. (2019) Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures. Genes
- Chang, Ching-Ho et al. (2019) Islands of retroelements are major components of Drosophila centromeres PLoS biology
- Jamy, Mahwash et al. (2019) Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity BioRxiv
- Kao, Tzu-Tong et al. (2019) Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae). Molecular phylogenetics and evolution
- Zhuang, Weijian et al. (2019) The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature genetics
- Hotaling, Scott et al. (2019) The rising tide of high-quality genomic resources. Molecular ecology resources
- Kronenberg, Zev N. et al. (2019) Extended haplotype phasing of de novo genome assemblies with FALCON-Phase BioRxiv
- Ananthasayanam, Sudhakar et al. (2019) First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis) 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
- Chen, Wenbo et al. (2019) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). GigaScience
- 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
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Minio, Andrea et al. (2019) Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3
- 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
- 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
- Kingan, Sarah and Carroll, Andrew (2019) Webinar: Variant calling and de novo genome assembly with PacBio HiFi reads
- Kingan, Sarah and McKernan, Kevin (2019) Webinar: Smoking out structural variants in the cannabis genome
- 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
- Application Brief: Targeted sequencing for amplicons – Best Practices (2019)
- Application Brief: Long-read RNA sequencing – Best Practices (2019)
- 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)
- 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)