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
- Tørresen, Ole K et al. (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic acids research
- Bickhart, Derek M et al. (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology
- Loit, Kaire et al. (2019) Relative Performance of MinION (Oxford Nanopore Technologies) vs. Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Applied and environmental microbiology
- Martijn, Joran et al. (2019) Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environmental microbiology
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- Jamy, Mahwash et al. (2019) Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity BioRxiv
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Mehta, Devang et al. (2019) A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic acids research
- Redondo, Miguel A et al. (2018) Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits. The ISME journal
- Beaulaurier, John et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature biotechnology
- Heeger, Felix et al. (2018) Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Molecular ecology resources
- Wen, Ming et al. (2018) Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing. GigaScience
- 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
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Mathew, Lolita G et al. (2018) ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-selected pink bollworm. Scientific reports
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Löber, Ulrike et al. (2018) Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human molecular genetics
- Zhu, Chunhui et al. (2018) Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection. Gene
- 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
- Xin, Tianyi et al. (2018) Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta pharmaceutica Sinica. B
- Zida, P.E. et al. (2018) Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens Crop protection
- Harumoto, Toshiyuki et al. (2018) Male-killing toxin in a bacterial symbiont of Drosophila. Nature
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful algae
- Hu, Yi et al. (2018) Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. Nature communications
- Magrini, Vincent et al. (2018) Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC genomics
- 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
- 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
- Lu, You et al. (2018) Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology
- 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
- Massonnet, Mélanie et al. (2018) Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. Molecular plant pathology
- Palmer, Jonathan M et al. (2018) Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Nature communications
- Poster: Baybayan, Primo et al. (2020) New advances in SMRT Sequencing facilitate multiplexing for de novo and structural variant studies
- Poster: Ekholm, Jenny et al. (2019) Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results
- 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
- Weber, Kay (2020) Webinar: Bioinformatics lunch & learn – HiFi assembly
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Wheeler, Nic (2019) User Group Meeting: Long-read RNA Sequencing in neglected human parasites
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Korlach, Jonas and Garimella, Kiran and Tallon, Luke and McCarthy, Shane (2019) Webinar: Sequence with Confidence – Introducing the Sequel II System
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- Pillai, Nisha (2018) Webinar: Assessing the targeted regions using a PacBio Amplicon analysis applications
- 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
- 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