- Course overview
- Search within this course
- Environmental DNA
- DNA metabarcoding and its applications
- Workflow for eDNA metabarcoding
- DADA2 for analysing metabarcoding data
- Statistics principles in data analysis
- Advances in biodiversity exploration
- Open data resources for eDNA
- Bringing data to life: Data management and sharing
- Further learning
- Your feedback
- References
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Reference databases for biodiversity studies
A reference database is a curated collection of genetic sequences from known organisms, often reviewed by taxonomic experts to ensure accuracy. Data from public repositories like NCBI or BOLD require curation due to frequent misidentifications. An ideal reference database offers broad taxonomic coverage, includes high-quality sequences (such as those obtained through Sanger sequencing), and provides accurate taxonomic annotations. Additionally, associated metadata enhances the utility of the database for biogeographic studies.
A few commonly used reference databases have been listed in the table below:
| Database name | Target gene | Target organisms | Reference | Database link |
| SILVA | 16S & 18S rRNA | Bacteria, Archaea, Protists, Fungi, Metazoa | Quast et al. 2013 | Silva (arb-silva.de) |
| PR2 | 18S rRNA | Protists, All eukaryotes | Guillou et al. 2013 | The PR2 databases (pr2-database.org) |
| UNITE | ITS | Fungi, All eukaryotes | Kõljalg et al. 2019 | UNITE (ut.ee) |
| MaarjAM | 18S rRNA ITS | Arbuscular mycorrhizal fungi | Öpik et. 2010 | https://maarjam.ut.ee/ |
| Midori2 | COI | All eukaryotes | Leray et al. 2012 | Home (reference-midori.info) |
| Mitofish | 12S | Fish | Zhu et al. 2023 | MitoFish: Mitochondrial Genome Database of Fish (u-tokyo.ac.jp) |
| 12S vertebrateClassifier | 12S | Vertebrates | Porter 2021 | https://github.com/terrimporter/12SvertebrateClassifier |
| Diat barcode | 18S rbcL | Diatoms | Rimet el. 2019 | GitHub – fkeck/diatbarcode: Access the diat.barcode database with R |
 Now that you’ve explored the metabarcoding workflow, conducted bioinformatics analysis with DADA2, and learned about assigning taxonomy, take a moment to reflect on your own project. Consider how you can adapt these methods in a way that is suitable and effective for your research. What insights or techniques can you incorporate? |
Next, as we shift our focus towards other important aspects of data-driven research, it’s essential to conduct a thorough statistical examination in big data analysis to ensure that your conclusions are valid. In the upcoming section, you will explore how to apply statistical methods specifically for biological interpretation.