The listing below is a collection of publications by the scientific community describing extraction protocols for high-molecular weight DNA followed by PacBio sequencing. When possible, the links point directly to the methods section (or supplementary information).
If you have protocols you would like to share, or have questions about DNA extraction for PacBio sequencing, please contact ExtractDNA@pacb.com. For general considerations, please check out our DNA Prep and Sample Prep Tech Notes.
Animals
- Invertebrates
- Jenkins2020 – Extracting quality DNA from marine invertebrates
- Panova2016 – DNA extraction protocols for whole-genome sequencing in marine organisms
- microinvertebrates
- arthropods
- arachnids
- Guerrero2019 – The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901
- Liu2019 – DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola
- Burgess2018 – Draft genome assembly of the sheep scab mite, Psoroptes ovis
- Randall2018 – The draft genome assembly of Dermatophagoides pteronyssinus supports identification of novel allergen isoforms in Dermatophagoides species
- Cramaro2017 – Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing
- Guerrero2019 – The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901
- crustaceans
- Liu2019 – Crab muscle extraction & sequencing (Circulomics application note)
- Baldwin-Brown2018 – A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome
- Gonçalves Athanasio2016 – Optimisation of DNA extraction from the crustacean Daphnia
- Liu2019 – Crab muscle extraction & sequencing (Circulomics application note)
- insects
- Geib2020 – Asian giant hornet (Vespa mandarinia) genome project
- Wouters2020 – Extraction of high molecular weight DNA from aphids and other sap-feeding insects for long-read sequencing
- Pippel2020 – A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)
- Kingan2019 – A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing
- Oppert2019 – Optimized Extraction of Insect Genomic DNA for Long-Read Sequencing
- Geib2020 – Asian giant hornet (Vespa mandarinia) genome project
- arachnids
- hemichordates
- tunicates
- cnidarians
- Wilding2020 – The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes and the question of sexual reproduction
- Jeon2019 – The Draft Genome of an Octocoral, Dendronephthya gigantea
- Gold2018 – The genome of the jellyfish Aurelia and the evolution of animal complexity
- Kim2018 – The genome of the giant Nomura’s jellyfish sheds light on the early evolution of active predation
- mollusks
- Angthong2020 – Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform
- Kenny2020 – The gene-rich genome of the scallop Pecten maximus
- Liu2019 – Aplysia extraction & sequencing (Circulomics application note)
- Zagrodzka2019 – PacBio protocol Littorina saxatilis
- Arseneau2017 – Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues
- Angthong2020 – Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform
- worms
- Wang2020 – Comprehensive Chromosome End Remodeling during Programmed DNA Elimination (Ascaris nematode)
- Serra2019 – Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
- Grohme2018 – The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms
- Grohme2018 – Small- and Large-Scale High Molecular Weight Genomic DNA Extraction from Planarians
- Rödelsperger2017 – Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus
- Wang2020 – Comprehensive Chromosome End Remodeling during Programmed DNA Elimination (Ascaris nematode)
- Jenkins2020 – Extracting quality DNA from marine invertebrates
- Vertebrates
- fish
- Adrian-Kalchhauser2020 – The round goby genome provides insights into mechanisms that may facilitate biological invasions
- Zagrodska2020 – DNA Extraction protocol for corkwing wrasse (Symphodus melops; September 2016 updated January 2020)
- Chen2019 – The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies
- Liu2019 – Fish skeletal muscle extraction & sequencing (Circulomics application note)
- Zhou2019 – Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data
- Adrian-Kalchhauser2020 – The round goby genome provides insights into mechanisms that may facilitate biological invasions
- amphibians
- reptiles
- birds
- He2020 – Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant
- Bernberg2020 – yellow-bellied sapsucker (ethanol-preserved tissue, additional pre-extraction notes) and red-breasted sapsucker (frozen tissue) (SMRT Leiden conference presentation)
- Formenti2019 – SMRT long-read sequencing and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)
- He2020 – Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant
- mammals
- fish
Plants
- Driguez2021 – LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology (with detailed extraction protocol)
- Li2020 – A simple plant high-molecular-weight DNA extraction method suitable for single-molecule technologies
- Mayjonade2016 – Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules
- Angiosperms
- Wang2021 – Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions (ref. 32)
- Liu2020 – Chromosome-level draft genome of a diploid plum (Prunus salicina)
- Castanera2020 – An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes
- Pucker2019 – A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
- Anderson2018 – Protocol- a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing
- Inglis2018 – Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high throughput SNP genotyping and sequencing applications
- Wang2021 – Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions (ref. 32)
- Gymnosperms
- Other
- Chen2020 – Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11
- Becker2020 – Phased Diploid Genome Sequence for the Fast-Growing Microalga Picochlorum celeri
- Shan2020 – First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies (edible seaweed)
- Arimato2019 – A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants (algae)
- Panova2016 – DNA extraction protocols for whole-genome sequencing in marine organisms (algae)
- Chen2020 – Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11
Fungi
- Schwessinger2020 – High quality DNA from Fungi for long read sequencing e.g. PacBio V.11
- Vasquez-Gross2020 – A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA
- Penouilh-Suzette2020 – A simple method for high molecular-weight genomic DNA extraction suitable for long-read sequencing from spores of an obligate biotroph oomycete
- Fountain2020 – Two New Aspergillus flavus Reference Genomes Reveal a Large 2 Insertion Potentially Contributing to Isolate Stress Tolerance and 3 Aflatoxin Production
- Faure2019 – Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum
- Nagappan2018 – Improved nucleic acid extraction protocols for Ganoderma boninense, G. miniatocinctum and G. tornatu
- Schwessinger2017 – Extraction of high molecular weight DNA from fungal rust spores for long read sequencing
- Solomon2016 – Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi
- Sonnenberg2016 – A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus
Protists
- Kawano-Sugaya2020 – Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica
- Tanaka2019 – Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein
- Mock2017 – Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus
Microbial
- Epperson2020 – A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells
- Gomez2019 – Methods for extracting ‘omes from microbialites
Disclaimer: PacBio does not assume any guarantees associated with the methods described in these publications. Groupings are meant to be pragmatic and not reflecting rigorous taxonomic categories. PacBio products are for Research Use Only, not for use in diagnostic procedures. Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, SMRTbell, and Sequel are trademarks of Pacific Biosciences. All other trademarks are the sole property of their respective owners. Please email ExtractDNA@pacb.com with any feedback.