This is a non-redundant database based on NCBI that contains all eukaryotic mitochondria and COI genes. It contains almost all mitochondrial sequences and COI sequences as of December 2021.
See pdf for the composition of the Venn diagram: venn.pdf (The number indicates the sequence number)
A non-redundant reference database of all mitochondrial and COI sequences for eukaryotes.
A non-redundant reference database containing only mitochondrial-related sequences for eukaryotes.
A non-redundant reference database containing only COI-related sequences for eukaryotes.
A characteristic database created with 57 common zooplankton genus recorded in the Three Gorges Reservoir area from historical records (not used in the article), for tutorials and testing. Smaller files are suitable for uploading to Github.
- mito/mitochondrial
Mainly focus on keywords "Mitochondrion" and "Mitochondrial" - COI
Mainly focus on keywords "COI" and "COX1" - 3xia.genus
More than 50 common genus in the Three Gorges Reservoir area - Euka/Eu
eukaryotic/eukaryotes - acc
NCBI accession ID, GenBank number - tax
taxonomy information - taxid
The classification number (ID) corresponding to each accession ID on NCBI - .qza
qza format files used for qiime2 analysis, including classification information files and reference sequence files - ref
reference - refseq
reference sequences in the Database - rmdup
Remove duplicate sequences based on 100% sequence similarity - lab
Title corresponding to each sequence on NCBI - .fasta
fasta format file
Please visit Folder "TutorialOnHowToUseAndBuildACustomDatabase" to learn how to use these databases we created, and create your own unique database.
1）Hu, H., Wei, X.-Y., Liu, L., Wang, Y.-B., Jia, H.-J., Bu, L.-K. and Pei, D.-S. (2023) Supervised machine learning improves general applicability of eDNA metabarcoding for reservoir health monitoring. Water Research 246, 120686.
doi:10.1016/j.watres.2023.120686
2）Hu, H., Wei, X.-Y., Liu, L., Wang, Y.-B., Bu, L.-K., Jia, H.-J. and Pei, D.-S. (2024) Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems. Applied Microbiology and Biotechnology 108(1), 1-17.
doi:10.1007/s00253-023-12993-4