Sequence the most challenging BACs
Scientists often use bacterial artificial chromosome (BAC) sequencing to close gaps in existing genome assemblies, or as a method of targeted sequencing to fine-map regions of interest. BAC clones containing GC- or AT-rich regions or repeat structures can be challenging for short-read sequencing technologies.
Complete BACs with confidence
With the long reads and uniform coverage of Single Molecule, Real-Time (SMRT) Sequencing, you can sequence and assemble finished BACs with high consensus accuracy – often into a single contig per BAC.
SMRT Sequencing on PacBio Systems gives you the ability to:
- Reconstruct medically and developmentally important structures within complex regions, such as the Y chromosome
- Finely map genes of interest with structural variation and haplotype information for evolutionary and agricultural studies
- Generate platinum-level genome assemblies
- Resolve historically difficult-to-sequence regions in draft genomes
- Pool dozens of BACs in a single SMRT Cell for efficient and cost-effective sequencing
Workflow: From BACs to a full view of the most complex regions
- Library preparation
- SMRT Sequencing on PacBio Systems
- Take advantage of the Sequel System to reduce project costs and generate ˜7X more reads compared with the PacBio RS II
- Achieve 10-15 kb average read lengths, with some reads as long as 60 kb
- Attain consensus accuracies >99.999% by avoiding mapping and systematic errors
- Scale throughput based on project needs; recommend 50X coverage for high-quality de novo genome assemblies
- Data analysis with SMRT Analysis or PacBio DevNet
- Generate de novo assemblies with HGAP algorithm within SMRT Analysis
- Additional bioinformatics resources on DevNet
Featured research: BAC sequencing to resolve structural variation in maize
Aluminum toxicity is the primary limitation for crop production on acidic soils, which make up 50% of the world’s potentially arable lands. In this study, scientists associated aluminum tolerance in maize with the presence of three copies of the MATE1 gene. This repeat-heavy region of the genome was fine-mapped using SMRT Sequencing of BACs, allowing scientists to explore the evolutionary basis of this variation and develop improved crops1.
Explore this research further.
To learn more about how SMRT Sequencing can resolve your challenging BAC sequencing projects, contact us.
- Maron, L.G. et al. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences. 110(13), 5241-5246.
- Koskinen, Lotta L E et al. (2015) Identification of a common risk haplotype for canine idiopathic epilepsy in the ADAM23 gene. BMC Genomics
- Antonacci, Francesca et al. (2014) Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nature Genetics
- Chen, Xiao et al. (2014) The architecture of a scrambled genome reveals massivel levels of genomic rearrangement during development. Cell
- Wang, Muhua et al. (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics
- Huddleston, John et al. (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research
- Chin, Chen-Shan et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods
- Maron, Lyza G et al. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences
- Carlier, Aurelien et al. (2015) The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environmental Microbiology
- Reichwald, Kathrin et al. (2015) Insights into sex chromosome evolution and aging from the genome of a short-lived fish. Cell
- Schwartz, John C et al. (2015) The assembly and characterisation of two structurally distinct cattle MHC class I haplotypes point to the mechanisms driving diversity. Immunogenetics
- Faber-Hammond, Joshua J et al. (2015) Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes. Genome Biology and Evolution
- Ng, Preston S K et al. (2014) Ferrets exclusively synthesize Neu5Ac and express naturally humanized influenza A virus receptors. Nature Communications
- Mensah, Martin A et al. (2014) Pseudoautosomal region 1 length polymorphism in the human population. PLoS Genetics
- Saïdou, Abdoul-Aziz et al. (2014) Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. Theoretical and Applied Genetics
- Akagi, Takashi et al. (2014) A Y-chromosome-encoded small RNA acts as a sex determinant in persimmons. Science
- Takehana, Yusuke et al. (2014) Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena. Nature Communications
- Bernardini, Federica et al. (2014) Site-specific genetic engineering of the Anopheles gambiae Y chromosome. Proceedings of the National Academy of Sciences
- Hall, Andrew Brantley et al. (2014) Insights into the preservation of the homomorphic sex-determining chromosome of Aedes aegypti from the discovery of a male-biased gene tightly linked to the M-locus. Genome Biology and Evolution
- Cowley, Allen W et al. (2014) Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats. Physiological Genomics
- Sudmant, Peter H et al. (2013) Evolution and diversity of copy number variation in the great ape lineage. Genome Research
- Presentation: Wing, Rod A et al. (2015) Old school/new school genome sequencing: One step backward — a quantum leap forward.
- Presentation: Guethlein, Libby et al. (2013) Genomic Architecture of the KIR and MHC-B and -C Regions in Orangutan
- Eichler, Evan (2014) ASHG PacBio Workshop: Resolving complexity of the human genome
- Brubaker, Shane (2014) PAG PacBio Workshop: Assembly, haplotyping, and annotation of a high GC algal genome