SMRT-Based Genome Sequencing

Overview

CD Genomics' single molecule, real-time sequencing (SMRT)-based microbial targeted and whole-genome sequencing services can help you with precise microbial identification, generation of complete reference genomes, comparative genomic studies, and genomic exploitation. The applications for SMRT-based genome sequencing vary. Just to list a few: accurate microbial identification, microbial genomic characterization, pathogen detection, environmental monitoring, and routine testing of raw materials for bacterial contamination.

Our Advantages:

Flexible sequencing strategies and bioinformatics pipelines.
Decades of experience in genomics services and innovative technology platforms.
Exceptionally long read lengths (20 kb or more) and unparalleled consensus accuracy.
Sequencing of the entire plasmid or virus in single reads, without the need for assembly.
Time-saving, and simplified workflow.

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Introduction to our SMRT-based genome analysis platform

The microbial genome is smaller than that of eukaryotes. Most bacteria have only one circular chromosome, with the exceptions of other bacteria with more than one (several linear chromosomes or combinations of circular and linear chromosomes). The presence of plasmids (the circular extra-chromosomal DNA and the bacterial genome) is another major characteristic of prokaryotic genomes, which mediating the rapid evolution of microorganisms and can be transferred by horizontal DNA transfer. Our SMRT-based genome sequencing, using technology from PacBio Biosciences, can provide accurate contiguous sequences for complete bacterial, viral, and fungal DNA or RNA genomes. The PacBio SMRT sequencing technology is characterized by unparalleled raw read accuracy, read length and read depth, which is helpful for the reconstruction of high-quality drafts and complete microbial genomes.

Based on the PacBio SMRT platform, we provide microbial targeted and whole-genome sequencing services to analyze challenging genomic regions like structural variants and repeat sequences for high-quality assemblies, perform accurate microbial identification, clarify the role of phage insertion, transposon insertion and other structural variants in the evolution of virulence, and recover plasmids to track transmission paths and drug resistance. Our SMRT-based genome analysis can be used to redefine the genetic and biochemical diversity in complex communities, elucidate virus-host interactions, uncover new taxonomic groups and metabolic capabilities, and determine how functions are distributed across environmental gradients.

SMRT-based genome analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes raw data quality control, genome annotation, gene function annotation, reference genome alignment, and custom analysis, which is flexible to your needs.

Pipeline	Content
Raw data quality control	Correction, classification, reduced redundancy, etc.
Genome annotation	Prediction of pathogenicity genes, susceptibility gene prediction, non-coding RNA prediction, detection of clustered regularly interspaced short palindromic repeats (CRISPRs), etc.
Gene function annotation	COG/GO/KEGG analysis, etc.
Comparative genomics	Construction of phylogenetic trees, divergence-time estimation, etc.
Custom analysis	More data mining upon your request.

Sample Requirement

1. DNA amount ≥ 2 μg, concentration ≥ 20 ng/μL
2. 1.8 < OD_260/280 < 2.0 without degradation and RNA contamination

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw data files in BAM format, demultiplex CCS reads in FASTQ format, quality-control dashboard, statistic data, and your designated bioinformatics analysis report.

References

Sonia Agrawal, et al. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. BMC Genomics. 2017; 18: 332.
J. Ronholm, et al. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev. 2016; 29(4): 837–857.
Miriam Land, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015; 15(2): 141–161.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.