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
- 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
- Roach, Michael J. et al. (2018) Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay BioRxiv
- 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
- Douglass, Alexander P et al. (2018) Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS Pathogens
- Marx, Vivien et al. (2018) What makes birds and bats the talk of the town. Nature Methods
- Nattestad, Maria et al. (2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Research
- Kronenberg, Zev N et al. (2018) High-resolution comparative analysis of great ape genomes. Science
- Gao, Fei et al. (2018) Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. GigaScience
- Kronenberg, Zev N et al. (2018) FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes BioRxiv
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human Molecular Genetics
- deCarvalho, Ana C et al. (2018) Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nature Genetics
- Ling, Hong-Qing et al. (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature
- Wang, Wensheng et al. (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature
- Harumoto, Toshiyuki et al. (2018) Male-killing toxin in a bacterial symbiont of Drosophila. Nature
- 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
- Xu, Qing et al. (2018) The genomic floral language of rose Nature Genetics
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful Algae
- Vincent, Antony T et al. (2018) Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing. Genome
- Sedlazeck, Fritz J et al. (2018) Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods
- Berná, Luisa et al. (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microbial Genomics
- Otto, Thomas D et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research
- Raymond, Olivier et al. (2018) The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics
- Sedlazeck, Fritz J et al. (2018) Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nature Reviews. Genetics
- Slager, Jelle et al. (2018) Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 BioRxiv
- Frank, Jeroen et al. (2018) Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing. Scientific Reports
- Hu, Yi et al. (2018) Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. Nature Communications
- Yadav, Vikas et al. (2018) RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Sciences of the United States of America
- 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
- Koren, Sergey et al. (2018) Complete assembly of parental haplotypes with trio binning BioRxiv
- Minio, Andrea et al. (2018) Isoform-scale annotation and expression profiling of the Cabernet Sauvignon transcriptome using single-molecule sequencing of full-length cDNA BioRxiv
- de Castro Nunes, Renata et al. (2018) Structure and distribution of centromeric retrotransposons at diploid and allotetraploid Coffea centromeric and pericentromeric regions. Frontiers in Plant Science
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Schwessinger, Benjamin et al. (2018) A near-complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high interhaplotype diversity. mBio
- Poster: Heiner, C. et al. (2018) Single chromosomal genome assemblies on the Sequel System with Circulomics high molecular weight DNA extraction for microbes
- Poster: Vogelsang, R. et al. (2018) Population-scale discovery of structural variants with PacBio SMRT Sequencing
- Poster: Vierra, M. et al. (2018) Characterizing the pan-genome of maize with PacBio SMRT Sequencing
- Poster: Blethrow, J. Sisneros, N. et al. (2018) Best practices for whole genome sequencing using the Sequel System
- 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: 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: 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
- (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 recipies for PacBio data
- Ameur, A. and Graves-Lindsay, T. and Peluso, P. (2018) Webinar: Assembling high-quality human reference genomes for global populations
- Korlach, Jonas (2018) Podcast: Why the diversity of genomic data matters
- (2018) Tutorial: Multiplexed Microbial Assembly [SMRT Link v5.1.0]
- Hoischen, A. and Wenger, A (2018) Webinar: Sequencing Structural Variants for Disease Gene Discovery and Population Genetics
- Renner, Tanya (2018) PAG Conference: Long-read sequencing reveals complex genomic architecture in independent carnivorous plant lineages
- Wenger, Aaron (2017) Video: Structural variant detection with SMRT 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 [SMRT Link v5.0.0]
- (2017) Tutorial: Structural variant calling [SMRT Link v5.0.0]
- 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
- 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
- (2017) Tutorial: HGAP4 de novo assembly 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
- 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, Maria (2016) Webinar: Analysis and visualization tools for long reads, assemblies and complex variation
- Application Note: Microbial multiplexing workflow on the Sequel System (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)
- 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)