On the basis of Operational Taxonomic Unit (OTU), our eukaryotic diversity analysis platform is dedicated to characterizing eukaryotic diversity in an efficient and economical manner. We utilize the advanced next/third generation sequencing technology in combination with molecular biology methods to support our clients in a variety of fields.
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Our integrated and novel platform enables high-throughput and reliable 18S/ITS analysis for eukaryotic diversity detection with a combination of sequencing technology (Sanger, Illumina MiSeq/HiSeq, and PacBio SMRT sequencing) and quantitative PCR (q-PCR). The principle of this platform is based on the role of 18S rRNA and ITS as molecular markers in eukaryotes. This platform allows both short-read 18S/ITS sequencing by Illumina MiSeq/HiSeq (such as the amplification and sequencing of V4 region of 18S rRNA) and full-length 18S/ITS sequencing by PacBio SMRT technology. The data need to be further validated by Sanger sequencing and q-PCR with genus- and species-specific primers. Quantitative PCR can also be used to quantify microbial strains. Based on our eukaryotic diversity analysis platform, we provide provide eukaryotic 18S rRNA sequencing and fungal ITS sequencing.
Our platform has supported a variety of fields, including basic research, clinical use, agriculture, environment, as well as pharmaceutical and food & beverage industries, etc. Our featured eukaryotic diversity analysis services include soil actinomycetes diversity analysis and clinical microbiology. In addition to eukaryotic diversity analysis platform, prokaryotic diversity analysis platform is also available for comprehensive microbial diversity detection by using 16S rRNA as molecular marker.
Our experts conduct reliable eukaryotic diversity analysis including species annotation, diversity analysis, evolutionary analysis, functional profiling, and correlation analysis. The following table shows the optional bioinformatics analyses at CD Genomics.
Table 1. Eukaryotic diversity analysis at CD Genomics.
|Bioinformatics analysis||Problems to be solved|
|Species annotation||OTU clustering, species annotation|
|Diversity analysis||α diversity||Species richness within a single microbial ecosystem|
|β diversity||Diversity in microbial community between different environments|
|Meta-analysis||Comparative studies of abundant features between datasets|
|Evolutionary analysis||Construction of phylogenetic tree|
|Functional analysis||Analysis of the Intestinal Microflora||Locate the gut bacteria, predict human disease, and provide disease treatment|
|PICRUSt||Predict functional profiles|
|FAPROTAX||Predict the process of biochemical cycles|
|Tax4fun||Predict functional profiles|
|FunGuild||Predict the ecological roles of eukaryotes|
|Correlation analysis||CCA||Study the relationships between microbes and environmental factors|
OD260/230 ≥ 1.8; 2.0, 1.8 < OD260/280 < 2.0, no degradation or contamination.
Illumina platform: DNA amount ≥ 300 ng, PCR Products ≥ 400 ng
PacBio platform: gDNA ≥ 100 ng, PCR Products ≥ 400 ng
Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, q-PCR data, statistic data, and your designated bioinformatics report.