DNA Barcoding Service

Overview

DNA barcoding, as a cutting-edge molecular technology, its core principle is to identify and classify species by leveraging the short standardized regions of DNA. This technology focuses on the unique genetic characteristics contained in specific DNA sequences, usually selecting mitochondrial (such as the COI gene in animals) or chloroplast (such as the rbcL or matK gene in plants) regions to construct exclusive "barcodes", thereby precisely distinguishing different species. DNA Barcoding has revolutionized biodiversity research, ecological studies, and conservation efforts by providing a rapid, accurate, and cost-effective means of species identification, even in cases where traditional morphological methods are challenging or impossible.

Our DNA Barcoding Service Enhances Your Research with:

• Advanced Sequencing Technologies: Employing state-of-the-art next-generation sequencing (NGS) platforms, such as Illumina MiSeq or HiSeq, we achieve high-throughput, high-accuracy sequencing of barcode regions, enabling the identification of even closely related species.
• Universal barcode regions: To ensure good compatibility and comparability between research work and existing databases, we select mature and widely recognized barcode regions, such as the COI region for animals and the rbcL/matK region for plants.
• Comprehensive reference database: Our services cover comparison and analysis with extensive and meticulously compiled DNA barcode reference databases (such as BOLD and GenBank) to ensure the accuracy of species allocation and facilitate the discovery of new taxonomic groups.
• Automated data analysis: By leveraging complex bioinformatics processes, we have automated sequence assembly, quality control, and species identification processes, effectively reducing manual operation steps and lowering the probability of potential errors.

What Is DNA Barcoding Analysis

This technology achieves the goal of rapid and accurate species identification by reading the unique specific DNA sequences of each species. Compared with traditional morphological identification methods, DNA barcoding, with its high efficiency and objectivity, has opened up a brand-new path for the field of biological identification. The working principle of DNA barcoding is to extract DNA from a small tissue sample, amplify the target DNA region with PCR, and then sequence it. The obtained DNA sequence is compared with the reference database of known barcodes to determine the species identity. This approach has revolutionized biodiversity research, conservation biology and environmental monitoring by identifying species in complex ecosystems, detecting mysterious species and tracking illegal wildlife trade. Its simplicity and versatility make DNA barcoding a powerful tool for understanding and protecting the world's biodiversity.

How to Measure

1. Sample Collection and Experimental Design

In terms of sample collection and experimental design, we have formulated comprehensive and detailed plans for different research subjects. The sample types are rich and diverse. Human samples include blood, saliva, oral swabs and FFPE tissues. Animal samples include blood, tissue biopsy, hair follicles, and also support non-invasive sampling through fecal DNA. During sampling, spatial replication captures geographical differences through multi-location sampling. Time replication re-samples at different times to monitor changes; Replication depth ensures that each species or population has 10 to 20 individuals, thereby achieving accurate species identification.

2. DNA Extraction and Barcode Region Amplification

When extracting DNA, high-quality DNA can be separated from the sample using commercial kits or standard laboratory protocols. Then, the concentration can be measured with a spectrophotometer, and the integrity can be evaluated by agarose gel electrophoresis, etc. In terms of barcode region amplification, first select universal or taxonomic group-specific primers for standardized regions, such as COI for animals, rbcL or matK for plants, then optimize PCR conditions to ensure specific and efficient amplification, and set up positive and negative controls to monitor contamination and amplification situations.

3. Sequencing and Data Generation

Any sequencing method inevitably has its advantages and limitations. Sanger sequencing performs well in low-throughput projects or in application scenarios where there is a specific demand for high-quality, long-read sequences. Next-generation sequencing (NGS), with its outstanding performance, has become the ideal choice for high-throughput projects. It has the ability to sequence multiple samples and barcode regions simultaneously. In the data quality control stage, sequence trimming is first carried out using software such as Trimmomatic and Cutadapt to remove low-quality bases. Then, use tools such as UCHIME to detect and remove chimeric sequences; Finally, the cleaned sequence is compared with the reference database or a consistent sequence is constructed using software such as MAFFT.

4. Species Identification and Barcode Analysis

When conducting species identification work, professional tools such as BLAST are needed to compare and analyze the obtained barcode sequences with authoritative databases such as BOLD and GenBank. At the same time, a reasonable similarity threshold should be set based on the actual situation. For instance, for the animal cytochrome c oxidase subunit I (COI) gene, the similarity should be set at no less than 97% to precisely determine the species identity. In the barcode analysis stage, the first step is to calculate the genetic distance of intraspecific and interspecific sequences, and use this data to evaluate the effectiveness of barcodes in species differentiation. Then, search for the gaps in the genetic distance distribution, identify the barcode gaps that distinguish intraspecific variations from interspecific differences, and thereby clarify the obvious distinctions between species.

5. Functional and Phylogenetic Analysis (Optional)

Functional Annotation

• Predict Gene Function: If the barcode region is part of a functional gene, use annotation tools (e.g., InterProScan, Blast2GO) to predict the biological function of the encoded protein.

Phylogenetic Analysis

• Construct Phylogenetic Trees: Use software like MEGA or RAxML to infer evolutionary relationships among species based on barcode sequences, providing insights into species evolution and taxonomy.

6. Visualization and Reporting

Key Visualizations

• Barcode Sequence Alignments: Display aligned barcode sequences to highlight variable regions and species-specific differences.
• Phylogenetic Trees: Visualize the evolutionary relationships among species based on barcode data.
• Species Diversity Plots: Show the distribution and abundance of species in a given ecosystem or sample set.

Figure 1: DNA Barcoding

What Can We do

Universal species identification: The precise key to DNA barcodes

By sequencing this short and conserved region of any organism, we can precisely determine its species identity even if traditional morphological methods fail due to similar appearances or the presence of hidden species.

Biodiversity research: A Powerful Boost from High-throughput barcodes

High-throughput barcodes play a crucial role in biodiversity research. We adopt high-throughput sequencing technologies such as next-generation sequencing (NGS), which can handle a vast number of DNA barcode samples simultaneously. This not only makes rapid and cost-effective biodiversity surveys a reality, but also helps us systematically catalog species diversity in ecosystems, monitor endangered populations in real time, and detect invasive species at an unprecedented speed and accuracy.

The cornerstone of global cooperation: Construction and protection of the barcode reference database

We are fully committed to the construction and maintenance of the comprehensive DNA barcode reference database. By continuously adding new barcode sequences from verified species, ensure that the identification system is always up-to-date and reliable. This database is like a "global hub" for biodiversity research and conservation, effectively promoting cooperation and exchanges on a global scale.

Our Advantages

• High-precision species identification: Unparalleled accuracy, eliminating ambiguity

By leveraging DNA barcoding technology, we have achieved unparalleled accuracy in the field of species identification. By deeply analyzing the unique standardized short DNA sequences of each species, this method can precisely distinguish closely related organisms, successfully eliminating the ambiguity problems existing in traditional morphological identification and setting a new benchmark for species recognition.

• Fast and cost-effective: Process simplification, cost reduction and efficiency improvement

DNA barcoding technology enables us to process samples in a fast and economical way. Unlike traditional lengthy and labor-intensive taxonomic research, this method only requires a small tissue sample to complete DNA extraction, amplification and sequencing.

• Data insight protection: Data empowerment, Scientific decision-making

By building a comprehensive DNA barcode database, we have contributed valuable data resources to global biodiversity conservation efforts. Our analysis can track species distribution, detect invasive species and monitor the health of ecosystems, helping policymakers and conservationists make informed decisions based on scientific data to effectively protect endangered species and safeguard natural habitats.

Applications

Species Identification and Biodiversity Monitoring

DNA barcodes, as key tools for species identification and biodiversity research, play an irreplaceable role. The traditional species identification methods based on physical characteristics are not only time-consuming but also highly subjective. In contrast, DNA barcodes, with their rapid, accurate and uniform characteristics, provide a more scientific and reliable way for species identification. Take tropical rainforest research as an example. Scientists can accurately identify insect species from tiny samples with the help of DNA barcoding technology, and then explore the biodiversity of the area in depth. In the Marine environment, it helps distinguish fish that look similar but have different genes, enhances our understanding of Marine life, and contributes to the protection of endangered or invasive species.

Food Safety and Authenticity Verification

DNA barcodes are also very important for ensuring food safety. For instance, in the seafood industry, cheap fish are often passed off as high-quality ones. Identifying different types of fish can protect consumers' rights and safeguard them from the health risks of undeclared allergens. In herbal products, it confirms the existence of the said plant species, ensures quality and prevents toxic or endangered plants from being included.

Demo

Figure 2: Association of the relative abundance of spider species from seven different families in mock communities of 46 different arthropod species, with the relative read count recovered for the species after sequencing. (Kennedy, 2020)

Case Study

FAQs