生物種内、生物種間の遺伝多型の特徴づけ
全ゲノムシークエンスは生物における完全なDNAの構成を明らかにし、遺伝的および後生的な多型により詳細な解像度をもたらします。現在の技術では、ゲノムシークエンスをするにはまずゲノムを小さく断片化し、その後でde novoアセンブリ、あるいは既存のリファレンス配列にマッピングすることで繋げ直すプロセスが使われています。パズルを解き明かすのと同様、大きなゲノム断片であれば繋げ直す作業も容易に行えます。
1分子リアルタイム (SMRT) シークエンスは、最も高精度なコンセンサス配列と均一なゲノムカバレッジをもたらすロングリードにより、断片化されたドラフトゲノムではなく、最も包括的なde novoアセンブリを可能にします。PacBioシステムがもたらす真の全ゲノムシークエンスは、SNP/SNVから構造多型、移動因子、ハプロタイプ、エピジェネティクス、そして複雑性の低い領域における多型まで、すべての種類のゲノム多型を包括的かつ高精度に検出することができます。
PacBioは全ゲノムシークエンスに包括的なソリューションと高度なアプリケーションを提供します
- 1回のランで完全な微生物ゲノムの特徴づけを実施
- 包括的な遺伝子探索のための動植物における高品質なリファレンスゲノム配列を決定
- 比類のないヒトゲノムde novoアセンブリを構築
- エピジェネティクス修飾を同時に検出
- 1塩基の解像度で様々なサイズの構造多型を検出
SMRTシークエンスProject Calculator
全ゲノムシークエンス用のプロジェクトCalculatorを使い、Sequel システム利用時の必要時間、材料を予測しましょう。
- 動植物ゲノムDe novoアセンブリ
- ヒトゲノム構造多型探索
Selected Resources
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Research
- Nowoshilow, Sergej et al. (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature
- Kjærbølling, Inge et al. (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proceedings of the National Academy of Sciences of the United States of America
- Fallon, Timothy R et al. (2017) Firefly genomes illuminate the origin and evolution of bioluminescence bioRxiv
- Lu, You et al. (2017) Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology
- Hobbs, Matthew et al. (2017) Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Scientific Reports
- Zhao, Guangyao et al. (2017) The Aegilops tauschii genome reveals multiple impacts of transposons Nature Plants
- Hickey, Luke et al. (2017) Hunting structural variants: Population by population Front Line Genomics Magazine
- Luo, Ming-Cheng et al. (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature
- Jayakumar, Vasanthan et al. (2017) Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Briefings in Bioinformatics
- Ichikawa, Kazuki et al. (2017) Centromere evolution and CpG methylation during vertebrate speciation. Nature Communications
- Hickey, L. et al. (2017) Structural variation offers new home for disease associations and gene discovery Drug Discovery and Development Magazine
- Zimin, Aleksey V et al. (2017) The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience
- Nell, Sandra et al. (2017) Genome and methylome variation in Helicobacter pylori with a cag pathogenicity island during early stages of human infection. Gastroenterology
- Rödelsperger, Christian et al. (2017) Single-molecule sequencing reveals the chromosome-scale genomic architecture of the nematode model organism Pristionchus pacificus. Cell Reports
- Teh, Bin Tean et al. (2017) The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics
- Conway, Jonathan M et al. (2017) Functional analysis of the Glucan Degradation Locus (GDL) in Caldicellulosiruptor bescii reveals essential roles of component glycoside hydrolases in plant biomass deconstruction. Applied and Environmental Microbiology
- Sayadi, Ahmed et al. (2017) The evolution of dark matter in the mitogenome of seed beetles. Genome Biology and Evolution
- Edwards, Joan E et al. (2017) PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges andopportunities. Frontiers in Microbiology
- Chaisson, Mark J.P. et al. (2017) Multi-platform discovery of haplotype-resolved structural variation in human genomes bioRxiv
- Bartling, Pascal et al. (2017) The composite 259-kb plasmid of Martelella mediterranea DSM 17316(T)-a natural replicon with functional RepABC modules from Rhodobacteraceae and Rhizobiaceae. Frontiers in Microbiology
- Dallery, Jean-Félix et al. (2017) Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics
- Korlach, Jonas et al. (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. GigaScience
- van Dam, Peter et al. (2017) A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. Scientific Reports
- Bao, Jiandong et al. (2017) PacBio sequencing reveals transposable element as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae. Molecular Plant
- Forde, Brian M. et al. (2017) SMRT Sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenic Escherichia coli isolates from a historic hemolytic uremic syndrome outbreak in Australia bioRxiv
- Nattestad, Maria et al. (2017) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line bioRxiv
- Teng, Jade LL et al. (2017) PacBio but not Illumina technology can achieve fast, accurate and complete closure of the high GC, complex Burkholderia pseudomallei two-chromosome genome Frontiers in Microbiology
- van Dam, Peter et al. (2017) The distribution of miniature impala elements and SIX genes in the Fusarium genus is suggestive of horizontal gene transfer. Journal of Molecular Evolution
- Sipos, Gyorgy et al. (2017) Genome expansion and lineage-specific genetic innovations in the world’s largest organisms (Armillaria) bioRxiv
- Stoesser, N et al. (2017) Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Scientific Reports
- Zautner, Andreas E et al. (2017) Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT Sequencing Journal of Antimicrobial Chemotherapy
- Thomas, Prasad et al. (2017) First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis. Infection, Genetics and Evolution
- Wlodarska, Marta et al. (2017) Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell Host & Microbe
- 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: Wenger, Aaron et al. (2018) Population-scale discovery of structural variants with PacBio SMRT Sequencing
- Poster: Concepion, C., et al. (2018) De novo assembly and preliminary annotation of the Schizocardium californicum genome
- Poster: Concepcion, G., et al. (2018) Structural variant detection in crops using PacBio SMRT Sequencing
- Poster: Kingan, S. et al. (2017) Structural Variant Detection with Low-Coverage PacBio Sequencing
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Hickey, L. et al. (2017) Detecting pathogenic structural variants with low-coverage PacBio sequencing.
- 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: Wenger, Aaron et al. (2017) Structural variant detection with low-coverage Pacbio sequencing
- 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: Sisneros, N. et al. (2017) Best practices for whole genome sequencing Using the Sequel System
- 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: 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: Watson, C. T. et al. (2016) Characterizing haplotype diversity at the immunoglobulin heavy chain locus across human populations using novel long-read sequencing and assembly approaches
- Poster: Wenger, A. et al. (2016) Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Poster: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- 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: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Muehling, Jill R et al. (2016) SMRT Sequencing of the alala genome
- Presentation: Nattestad, Maria et al. (2015) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing
- Poster: Sedlazeck, Fritz J. et al. (2015) Detection of structural variants using third generation sequencing
- Poster: Rescheneder, Philipp et al. (2015) Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis
- Poster: Lee, Hayan et al. (2015) The resurgence of reference quality genome
- Presentation: Lindsay, Tina et al. (2015) ASHG – GRC Workshop
- Presentation: Meltz Steinberg, Karen et al. (2015) Building a platinum human genome assembly from single haplotype human genomes generated from long molecule sequencing
- 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
- Wenger, Aaron (2017) Video: Structural variant detection with SMRT Sequencing
- Jacob, Howard (2017) Podcast: Huh? 30 Million Americans Have a Rare Disease? Howard Jacob on the State of Clinical Sequencing
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- Brunner, Han (2017) ASHG PacBio Workshop: Long-read sequencing for detecting clinically relevant structural variation
- Lee, Charles (2017) ASHG PacBio Workshop: Multiplatform Discovery of Haplotype-Resolved Structural Variation in Human Genome
- Korlach, Jonas (2017) ASHG PacBio Workshop: PacBio Applications Updates & Future Roadmap
- Wenger, Aaron (2017) Webinar: Detecting Structural Variants in PacBio Reads – Tools and Applications
- (2017) Tutorial: Minor Variant Analysis
- (2017) Tutorial: Structural Variant Calling
- Wenger, Aaron (2017) Webinar: Structural Variant Detection in SMRT Link 5 with PBSV
- Kingan, Sarah (2017) Webinar: Understanding, curating, and analyzing your diploid genome assembly
- Singh, Siddharth (2017) Webinar: Beginner’s Guide to PacBio SMRT Sequencing Data Analysis
- 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
- Korlach, Jonas (2017) AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs
- Schatz, Michael (2017) AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples
- Glyllensten, Ulf (2017) AGBT Virtual Poster: Generation of local reference genomes using PacBio and BioNano data, and analysis of the “dark matter” of structural variants in 1000 Swedish genomes
- 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: HGAP4 de novo assembly application
- 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
- Korlach, Jonas (2016) ASHG PacBio Workshop: A future of high-quality genomes, transcriptomes, and epigenomes
- Ashley, Euan (2016) ASHG PacBio Workshop: Towards precision medicine
- Wenger, A. and Kujawa, S. and Hickey, L. and Chin, J. and Korlach, J. (2016) ASHG Virtual Poster: Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Wenger, Aaron (2016) Video: Using the Integrative Genomics Viewer (IGV) to visualize PacBio long-read SMRT Sequencing data
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Nattestad, Marie (2016) Webinar: Analysis and visualization tools for long reads, assemblies and complex variation
- Carroll, Andrew (2016) DNAnexus Webinar: Accurate calling of structural variation in PacBio data
- Application Brief: Low-coverage, long-read whole genome sequencing for structural variation – Best Practices. (2018)
- Application Brief: Large genome whole genome sequencing – Best Practices. (2018)
- De Novo Assembly Brochure: Assembly Options for your SMRT Sequencing Data (2018)
- Sequel System Brochure: The premier solution for long-read sequencing. (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)
- Product Note: Fast, high-resolution DNA Sizing with the Fragment Analyzer system (2016)