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Pacbio SMRT Sequencing

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Pacbio SMRT Sequencing

2021-08-05

Long-Read Metagenomic Sequencing
Microbial Whole Genome de novo Sequencing
Full-Length Transcripts Sequencing (Iso-Seq)
Human Whole Genome PacBio SMRT Sequencing
Plant/ animal Whole Genome PacBio SMRT Sequencing
Full-Length16S/ 18S/ ITS Amplicon Sequencing

Metagenomics sequencing is the way to do genomic analysis of microbial DNA fromenvironmental communities. It enables the population analysis of un-culturableor previously unknown microbes and allows researchers to comprehensively sample all genes in all organisms present in a given complex sample.
Now Jenker provides long-read metagenomicssequencing service on PacBio SMRT System in a culture-free method. Long-read metagenomics sequencing help scientists generating new insights into thefunction and pathway facets of the microbiome, trying to understand andelucidate the relations between microbes and its habitat/ host. Long-read metagenomics sequencing is a powerful way to obtain microbial genomes with the highest accuracy and reliability.
Key Features and Advantages

Longest average read lengths, with~50% of reads longerthan 50kb, which exceeds the size of repetitive elements in the averagebacterial genome.
Identify full-length genes within a microbial community using long-read metagenomic profiling with no assembly required
No DNA amplification.
Highest consensus accuracy, low sequencing-context bias

Bioinformatics Analysis

Gene prediction
Non-redundant Gene Catalog
Functional annotation: KEGG, eggNOG, CAZy.
Taxonomic annotation
Pathway, Heatmap, PCA, Clustering.
…

(More upon request)
Analysis Workflow

Jenker is providing PacBio Single Molecular Real-Time (SMRT) sequencing for microbial whole genome sequencing toget a comprehensive view of the microbial genome.
SMRT Sequencing haslong reads (average >15,000 bp, some reads >100,000 bp) and the highest consensus accuracy. It is especially helpful for genome de novo assembly. As we know, repetitive stretches of DNA are abundant and are one of the main technical challenges that hinder accurate sequencing and genome assemblyefforts. In the case of bacteria, the rRNA gene operon is often the largest region of repetitive sequence and range in size between 5 and 7 kb. Microbial whole genome sequencing by illumina HiSeq platforms utilizes sequencing by synthesis technology which islimited by its read length (50 to 300 bp), and as it requires PCR amplification of multiple DNA templates before sequencing which potentially increase base-composition bias.
With SMRT Sequencing on the Sequel System, there is no need sacrifice quality for affordability when assembling bacterialgenomes. Go well beyond draft-quality to achieve reference-quality assemblies,closing even the most repeat-dense and GC-rich genomes and resolving plasmids.
The advantage of SMRT long reads, which can overcome the problem of abnormal GC and high duplication of micorbial genomes, oftenassembled into a single contig. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing.
Key Features and Advantages

Generate platinum-standard, closedreference genomes
Affordably assemble gold-standardgenomes
Clarify the role of transposons,phage insertions, and other structural variants in the evolution of virulence
Recover plasmids to track drugresistance and transmission paths

Bioinformatics Analysis

Data quality control
Assembly
Genome Annotation
Functional Annotation
Comparative Genomics
Evolutionary Analysis

Analysis Workflow

Changes inisoform variants and relative abundancies are an important clue in deciphering how genomic variants drive the phenotypic differences between health anddisease. Only long-read sequencing can provide unbiased, direct detection ofall the isoforms present in the samples. Iso-Seq analysis allowus to generate full-length cDNA sequences without assembly. It characterizetranscript isoforms within targeted genes or across an entire transcriptome.
Key Features and Advantages

Discover new genes, transcripts and alternative splicing events
Improve genome annotation to identify gene structure, regulatory elements,
and coding regions
Increase the accuracy of RNA-seq quantification with isoform-level resolution

Sequencing Platforms
PacBio Sequel
Bioinformatics Analysis

Data Quality Control
Annotation of Gene Function, CDS Prediction and SSR Detection
Expression and Differential Expression
GO and KEGG
...

(More upon request)
Analysis Workflow:

Human Whole Genome PacBio SMRT Sequencing

Jenker is providing PacBio SMRT sequencing for human whole genome sequencing to reveal structural variants and produce directvariant phasing information across haplotype blocks and methylation.
Through SMRT sequencing, de novo genome assemblies deliver megabase-size contig N50s, consensus accuracies above 99.99%, and phased haplotypes so scientists can generate reference-quality assemblies of diverse populations to better understand the complexity of human health and disease.
Key Featuresand Advantages

Generate references unique to apopulation, individual or disease.
Generate fully phased haplotypesto identify common alleles in the population
Access novel types of geneticvariation and difficult-to-characterize regions
Use novel reference sequencesto improve variant detection in population specific loci

BioinformaticsAnalysis

Data quality control
Reference genome alignment
Genome preliminarily assembles
Genome annotation
SNP/ Indel identification and annotation
CNV/ SV identification and annotation
...

(More analysis upon request)
Analysis Workflow

Jenker is providing PacBio SMRT sequencing for animal/plant wholegenome sequencing to build better genomes and lead to the breakthroughdiscovery.
PacBio denovo genome assemblies deliver megabase-size contigN50s, consensus accuracies above 99.99%, and phased haplotypes so scientists cando more biology – capturing undetected SNVs, fully intact genes, and regulatoryregions embedded in complex structures.
Key Features and Advantages

generate high-quality denovo assemblies of genomes,
Call the broadest range of structural variant types
discover small variants and phase haplotypes

Bioinformatics Analysis

Data quality control
Genome preliminarily assembles
Genome function annotation,gene structure annotation, repeat sequence annotation and ncRNA annotation
Expansion and Contraction of gene family
Phylogenetic analysis
Genome-wide synteny analysis
Estimation of species divergence time
...

(More analysis upon request)
Analysis Workflow

Over the past 10 years, 16S/18S/ITS rRNA gene sequencing is the best tool to study bacterial and fungal taxonomy and molecular phylogeny.By taking advantage of PacBio SMRT long reads sequencing technology, Jenker can provide full-length 16S/18S/ITS rRNA sequencing service to helpyour research.
Take 16S rRNA as an example, the average read lengthof the PacBio SMRT sequences is 10~18 K, which can cover all variable areas of16S rRNA (the total length is around 1,500 bp). Meanwhile, circular consensussequencing (CCS) produces high intra-molecular consensus accuracy forfull-length 16S rDNA to achieve accurate to “species” classification andidentification.
18S rRNA (total length 1,500-2,000 bp) and ITS (about400-900 bp) are also able to be performed by full-length sequencing formicrobiome analysis.
Key Featuresand Advantages