Ribosome 18S rRNA Sequencing & Assembly Service
Are you currently grappling with the hurdles of precisely identifying eukaryotic microorganisms, conducting a thorough analysis of intricate microbial communities? At Creative Biolabs, our 18S rRNA sequencing & assembly service is here to propel your scientific discoveries forward. By leveraging cutting-edge next-generation sequencing (NGS) technologies and powerful bioinformatics tools, it empowers you to gain high-resolution insights into the rich tapestry of eukaryotic diversity.
Overview of 18S rRNA Sequencing & Assembly
The 18S ribosomal RNA (rRNA) is a fundamental component of the small ribosomal subunit in all eukaryotic organisms, serving as a cornerstone for phylogenetic analysis and biodiversity studies. Its ubiquitous presence, coupled with alternating conserved and variable regions, makes it an ideal molecular marker for identifying and classifying a vast array of eukaryotes, from fungi and protists to plants and animals. 18S rRNA sequencing, particularly utilizing high-throughput NGS technologies, overcomes the limitations of traditional culture-dependent methods by enabling comprehensive, unbiased detection of both culturable and unculturable eukaryotic microbes. This molecular approach has revolutionized fields such as microbial ecology, environmental science, and human health, providing unparalleled insights into eukaryotic community structure, dynamics, and their interactions within complex ecosystems.
Fig.1 Schematic illustration of the effect of rRNA expansion sequences on the selection of translation initiation sites.1
Key Procedures
Our 18S rRNA sequencing & assembly workflow is meticulously designed for clarity, precision, and efficiency, guiding your project from sample submission to comprehensive data analysis. Key steps involved:
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Initial Consultation & Project Design
Our expert team collaborates with you to understand your specific research objectives, sample types, and desired outcomes. We assist in designing the optimal sequencing strategy, including target regions, sequencing depth, and bioinformatics requirements. -
Sample Quality Control (QC) & DNA Extraction
Upon receiving your samples, rigorous quality control checks are performed to assess DNA integrity and concentration. If needed, Creative Biolabs offers advanced DNA extraction services optimized for challenging sample matrices to ensure high-quality template DNA for subsequent steps.
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PCR Amplification & Library Preparation
The conserved and variable regions of the 18S rRNA gene are amplified using highly specific primers. Our optimized PCR protocols minimize bias, ensuring accurate representation of the eukaryotic community. Subsequently, sequencing libraries are prepared.
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Sequencing Procedures
Prepared libraries are sequenced on high-throughput NGS platforms. This generates millions of high-quality paired-end reads, providing the depth necessary for robust taxonomic classification and diversity analysis.
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Bioinformatics Analysis & Assembly
Raw sequencing reads undergo stringent quality filtering, including trimming of adapters and low-quality bases, followed by merging of paired-end reads.
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Data Interpretation & ReportingBeyond basic taxonomic assignment, our bioinformatics pipeline includes advanced analyses such as alpha and beta diversity metrics to assess richness and evenness within samples and community dissimilarity between samples.
Finalized Project Outputs
- Processed Sequence Data
Quality-filtered and merged FastQ files, ready for further analysis.
- Detailed Taxonomic Classification Report
A comprehensive breakdown of eukaryotic taxa identified, including abundance information at various taxonomic levels.
- Diversity Analysis Metrics & Plots
Alpha diversity indices and beta diversity plots to compare and contrast microbial communities across your samples.
- Phylogenetic Tree
A visual representation of the evolutionary relationships among the identified eukaryotic groups.
Applications
1. Environmental Ecology
Characterizing eukaryotic microbial diversity in diverse ecosystems such as soil, fresh and marine waters, sediments, and air, for environmental monitoring and impact assessment.
2. Agricultural Science
Identifying fungal pathogens, beneficial microorganisms, and algal components in agricultural soils, plant microbiomes, and aquaculture systems to improve crop health and yield.
3. Bioremediation Studies
Investigating eukaryotic communities involved in the degradation of pollutants in contaminated environments.
4. Food and Beverage Industry
Detecting and identifying spoilage organisms (e.g., yeasts, molds) or beneficial eukaryotic microbes in food production and fermentation processes.
5. Biomedical Research
Analyzing eukaryotic components in human and animal microbiomes, particularly focusing on fungal and parasitic infections or host-microbe interactions.
6. Biotechnology & Bioprocessing
Monitoring eukaryotic populations in bioreactors and industrial fermentations to optimize processes and ensure product quality.
7. Marine Biology
Exploring phytoplankton and zooplankton diversity in marine environments, crucial for understanding ocean health and nutrient cycling.
Why Partner with Us?
- Cutting-Edge Technology
We leverage state-of-the-art NGS platforms and advanced long-read sequencing capabilities, ensuring high-fidelity sequencing and the ability to resolve complex eukaryotic communities, including those with challenging genomic features.
- Expert Bioinformatics
Our in-house team of experienced bioinformaticians utilizes robust, validated pipelines and access to continually updated reference databases, providing accurate taxonomic assignment, comprehensive diversity analysis, and customized data visualization.
- Comprehensive Quality Control
Rigorous quality control is embedded at every stage, from DNA extraction and library preparation to sequencing and data processing, guaranteeing the reliability and reproducibility of your results.
- Dedicated Scientific Support
We offer personalized consultations and ongoing technical support, ensuring that our services are perfectly aligned with your research goals and that you fully understand your data.
FAQs
Q: How does 18S rRNA sequencing compare to 16S rRNA or ITS sequencing?
A: While 16S rRNA sequencing targets prokaryotes and ITS sequencing is primarily used for high-resolution fungal identification, 18S rRNA sequencing offers a broader view of eukaryotic diversity. It's the go-to method when you need to characterize the entire eukaryotic microbial community, providing a robust framework for taxonomic and phylogenetic studies across various eukaryotic kingdoms.
Q: What kind of samples are suitable for 18S rRNA sequencing?
A: Our service is highly versatile and can accommodate a wide range of sample types. Common samples include environmental matrices like soil, water, sediment, and air filters. We also process biological samples such as gut contents, plant tissues, and isolated eukaryotic cultures. During our initial consultation, we can discuss the optimal sample collection and handling for your specific project.
Q: What level of taxonomic resolution can I expect from 18S rRNA sequencing?
A: 18S rRNA sequencing generally provides robust taxonomic resolution at the family, order, and sometimes genus level for a broad array of eukaryotes.
Q: How can Creative Biolabs ensure the quality and accuracy of the 18S rRNA sequencing data?
A: At Creative Biolabs, quality and accuracy are paramount. We implement stringent quality control measures at every stage, from verifying incoming sample integrity and optimizing DNA extraction to meticulous library preparation and running on high-fidelity sequencing platforms. Our bioinformatics pipelines incorporate advanced algorithms for error correction, read merging, and taxonomic assignment against curated databases, ensuring reliable and reproducible results for your research.
Our 18S rRNA sequencing & assembly provide an indispensable tool for researchers aiming to comprehensively understand eukaryotic microbial communities. By offering high-resolution taxonomic identification, robust diversity analysis, and clear phylogenetic insights, Creative Biolabs empowers your projects with the precision needed for groundbreaking discoveries in environmental science, clinical research, agricultural biology, and beyond. Ready to advance your research with unparalleled insights into eukaryotic diversity? Our team of experts is eager to discuss your specific project needs.
Reference
- Lindahl, Lasse. "Ribosome Structural Changes Dynamically Affect Ribosome Function." International Journal of Molecular Sciences 25.20 (2024): 11186. DOI: 10.3390/ijms252011186. Distributed under Open Access license CC BY 4.0, without modification.
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