Capture regions of interest in high resolution
Combining PacBio long-read sequencing with targeted sequence capture or bacterial artificial chromosomes (BACs) provides a powerful tool for a comprehensive view of specific genomic regions of interest, regardless of size.
Single Molecule, Real-Time (SMRT) Sequencing offers a flexible solution for targeting regions of interest, from several hundred base pairs to 20 kb, and delivers the most comprehensive view of the associated genes. With high-fidelity, long reads (>99% single-molecule read accuracy) it also delivers the read length and accuracy needed to improve fine mapping and simplify the assembly of complex portions of the genome. SMRT Sequencing gives you the ability to:
- Rapidly screen and identify all variants
- Discover haplotype-specific markers
- Resolve difficult-to-sequence regions, regardless of size
- Confirm insertion sites of transgenes and validate gene editing events
 | Sample & Library Preparation |
| Obtain targeted sequences with flexible sample and library workflows |
 | Sequencing |
| Maximize output and turn-around time with adjustable run parameters on the Sequel System. |
 | Data Analysis |
| Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet. |
Application Brief: Learn more about these best practices for targeted sequencing
Spotlight: Codfish study employs target capture to explore evolution
Researchers used SMRT Sequencing and Roche NimbleGen target capture to resolve the copy number variation and organization of hemoglobin (Hb) genes and their flanking regions across eight species of codish. Explore this research further:
Khang Hoff, S.N., et al., 2018. Long-read sequence capture of the hemoglobin gene clusters across species. bioRxiv, Preprint.
Spotlight: Amplicon sequencing on a massive scale
Scientists used SMRT Sequencing to characterize cytochrome c oxidase I in amplicons from 20,000 unique arthropod specimens as part of the efforts to DNA fingerprint and register species to better understand biodiversity. This work revealed that through multiplexing of samples, the Sequel System enables sequencing of millions of samples per year. Explore this research further:
Hebert, P.D.N. et al., 2018. A Sequel to Sanger: amplicon sequencing that scales. BMC genomics, 19(1), p.219.
Selected Resources
- 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
- Hoff, Siv Nam Khang et al. (2018) Long-read sequence capture of the hemoglobin gene clusters across gadid species. Molecular ecology resources
- Bull, Simon E et al. (2018) Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch. Science advances
- Borel, Florie et al. (2018) Editing out five Serpina1 paralogs to create a mouse model of genetic emphysema. Proceedings of the National Academy of Sciences of the United States of America
- Verhey, Theodore B et al. (2018) Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline. Molecular microbiology
- Zimmer, Christoph T et al. (2018) Neofunctionalization of duplicated P450 genes drives the evolution of insecticide resistance in the brown planthopper. Current biology
- Halo, Julia V et al. (2019) Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology
- Chien, Chih-Cheng et al. (2019) Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan. Scientific reports
- Arora, Heena et al. (2019) BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida bioRxiv
- Ma, Ke-Yi et al. (2019) Construction of a genomic Bacterial Artificial Chromosome (BAC) library for the prawn Macrobrachium rosenbergii and initial analysis of ZW chromosome-derived BAC inserts. Marine biotechnology
- Serpas, Lee et al. (2019) Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA. Proceedings of the National Academy of Sciences of the United States of America
- Patterson, Eric L et al. (2018) Glyphosate resistance and EPSPS gene duplication: Convergent evolution in multiple plant species. The Journal of heredity
- Brashear, Wesley A et al. (2018) Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation. Genome research
- Wei, Kang et al. (2018) A coupled role for CsMYB75 and CsGSTF1 in anthocyanin hyperaccumulation in purple tea. The Plant journal
- Kawato, Satoshi et al. (2018) Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus. Journal of virology
- Aw, Wen C et al. (2018) Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS genetics
- Jeong, Hyo-Bong et al. (2018) Single-molecule real-time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.). Plant biotechnology journal
- Klymiuk, Valentina et al. (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nature communications
- Wu, Yongzhen et al. (2018) Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice. Nature communications
- Gautier, Mathieu et al. (2018) The genomic basis of color pattern polymorphism in the Harlequin ladybird. Current biology
- Turner, Joe et al. (2018) The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti. Parasites & vectors
- Van Ghelder, Cyril et al. (2018) Ma orthologous genes in Prunus spp. shed light on a noteworthy NBS-LRR cluster conferring differential resistance to root-knot nematodes. Frontiers in plant science
- Zhang, Zhaogui et al. (2018) A PECTIN METHYLESTERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility. Nature communications
- Baltrušis, Paulius et al. (2018) Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR. International journal for parasitology
- Harazim, Markéta et al. (2018) Natural selection in bats with historical exposure to white-nose syndrome BMC zoology
- Emeriewen, Ofere Francis et al. (2018) Towards map-based cloning of FB_Mfu10: identification of a receptor-like kinase candidate gene underlying the Malus fusca fire blight resistance locus on linkage group 10. Molecular breeding
- Li, Da et al. (2018) Analysis of the Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health-related traits of common wheat. The Plant journal
- Keeble-Gagnère, Gabriel et al. (2018) Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome biology
- Slesarev, Alexei et al. (2018) CRISPR/Cas9 targeted capture of mammalian genomic regions for characterization by NGS BioRxiv
- Garsmeur, Olivier et al. (2018) A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature communications
- Nishiyama, Tomoaki et al. (2018) The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell
- Xing, Liping et al. (2018) Pm21 from Haynaldia villosa encodes a CC-NBS-LRR protein conferring powdery mildew resistance in wheat. Molecular plant
- Padmarasu, S et al. (2018) Identification of a leucine-rich repeat receptor-like serine/threonine-protein kinase as a candidate gene for Rvi12 (Vb)-based apple scab resistance Molecular breeding
- Hans, Jörg B et al. (2018) Discovery of gorilla MHC-C expressing C1 ligand for KIR. Immunogenetics
- Peng, Shuang et al. (2018) Enrichment of the antibiotic resistance gene tet(L) in an alkaline soil fertilized with plant derived organic manure. Frontiers in microbiology
- 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
- Presentation: Berges, Helene et al. (2016) Long read sequencing technology to solve complex genomic regions assembly in plants
- Poster: Gu, Jenny et al. (2016) Targeted sequencing of genes from soybean using NimbleGen SeqCap EZ and PacBio SMRT Sequencing
- Pillai, Nisha (2018) Webinar: Assessing the targeted regions using a PacBio Amplicon analysis applications
- 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
- (2017) Tutorial: Long amplicon analysis application [SMRT Link v5.0.0]
- Wing, Rod (2017) PAG PacBio Workshop: Introducing 5 new high-quality PacBio genome assemblies for rice to help solve the 10-billion people question
- Ranade, Swati (2016) AGBT Virtual Poster: Immune regions are no longer incomprehensible with SMRT Sequencing
- Berges, Hélène (2016) PAG Conference: Long reads sequencing technology to solve complex genomic regions assembly in plants
- PacBio Certified Service Providers (2018)
- Application Brief: Targeted sequencing for amplicons – Best Practices (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center (2017)
- Application Note: Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies (2016)
- Certified Service Provider Profile: Institute for Genome Sciences expands long-read sequencing services with new Sequel System (2016)
- Application Note: Targeted sequencing and chromosomal haplotype assembly using Cergentis TLA technology with SMRT Sequencing (2016)