Exploring microbiota impacting plant and animal health
To understand these interactions, complete genetic characterization of microbes is needed to drive improvements in crop yields, advance livestock health and production, and further preservation of wild animals and natural habitats.
Single Molecule, Real-Time (SMRT) Sequencing delivers a complete view of the microbiota impacting plant and animal health, growth, and production. The PacBio Systems enable scientists to:
- Resolve entire microbial genomes including their mobile elements
- Understand complex microbial communities with species-level resolution
- Characterize epigenetic modifications
- Investigate viral pathogenicity and transmission
- Discover novel genes and transcript isoforms
Spotlight: Species-level resolution of marine microbiomes
Scientists explored the complex ecosystem of coral-associated bacterial communities to understand their diversity and structure in the Indo-Pacific. PacBio full-length 16S rRNA sequences revealed a conserved profile of bacteria across diverse habitats. Explore this research further:
Pootakham, W. et al., 2017. High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Scientific Reports, 7(1), p.2774.
Spotlight: Phylogenetic analysis uncovers variation within a bacterial species
Scientists used whole genome sequencing to compare bacterial isolates from cattle. Their study revealed large within-species variation caused by changes in gene number and structural rearrangement that impact strain pathogenicity. Explore this research further:
Dickey, A.M. et al., 2016. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary Research, 47(1), p.31.
Selected Resources
- Magrini, Vincent et al. (2018) Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC Genomics
- Fallon, Timothy R et al. (2017) Firefly genomes illuminate the origin and evolution of bioluminescence BioRxiv
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- Lu, You et al. (2017) Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology
- Verhey, Theodore B et al. (2017) Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline. Molecular Microbiology
- Whitfield, Zachary J et al. (2017) The diversity, structure, and function of heritable adaptive immunity sequences in the Aedes aegypti genome. Current Biology
- Jayakumar, Vasanthan et al. (2017) Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Briefings in Bioinformatics
- Fraiture, Marie-Alice et al. (2017) An integrated strategy combining DNA walking and NGS to detect GMOs. Food Chemistry
- Wooddell, Christine I et al. (2017) RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg. Science Translational Medicine
- 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
- 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
- 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
- Kim, Hyeongmin et al. (2017) Characterization of the Rosellinia necatrix transcriptome and genes related to pathogenesis by single-molecule mRNA sequencing. The Plant Pathology Journal
- 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
- Thomas, Prasad et al. (2017) First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis. Infection, Genetics and Evolution
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Miller, Jason R. et al. (2017) Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation BioRxiv
- Pasini, Erica M et al. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Research
- Pootakham, Wirulda et al. (2017) High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Scientific Reports
- Tate, Heather et al. (2017) Comparative analysis of extended-spectrum-ß-lactamase CTX-M-65-producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States. Antimicrobial Agents and Chemotherapy
- Cox, Kevin L et al. (2017) TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton. Nature Communications
- Koren, Sergey et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research
- Andino, Raul et al. (2017) Long-read assembly of the Aedes aegypti genome reveals the nature of heritable adaptive immunity sequences BioRxiv
- Meng, Xiangli et al. (2017) Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerging Microbes and Infections
- Derbyshire, Mark et al. (2017) The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biology and Evolution
- Kuang, Zheng et al. (2017) The dynamic landscape of fission yeast meiosis alternative-splice isoforms. Genome Research
- Seong, Hoon Je et al. (2016) Methylome analysis of two Xanthomonas spp. using Single-Molecule Real-Time Sequencing. The Plant Pathology Journal
- Oren, Matan et al. (2016) Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family. BMC Genomics
- Karl, Julie A et al. (2016) Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities BioRxiv
- Chin, Chen-Shan et al. (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods
- Suzuki, Yuta et al. (2016) AgIn: Measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics
- Mayjonade, Baptiste et al. (2016) Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. BioTechniques
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- 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: 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: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Poster: Heiner, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- 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
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Hannigan, Brett (2016) DNAnexus Webinar: Simplifying de novo assembly with PacBio tools available on DNAnexus: FALCON
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Heiner, Cheryl (2016) AGBT Virtual Poster: Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Heiner, Cheryl (2016) AGBT Virtual Poster: Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Chin, Jason (2016) PAG Conference: Diploid genome assembly and comprehensive haplotype sequence reconstruction
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)
- Plant and Animal Sciences Brochure: A comprehensive view of genetic diversity (2017)
- Targeted Sequencing Application Brochure: Capture your regions of interest in high resolution. (2015)