May2023 reference datasets for Mitohelper (deduplicated)

Reference datasets (May2023 update) for Mitohelper (https://github.com/aomlomics/mitohelper)

Update (Jun2022): 251 erroneous duplicated records in the 12S rRNA data file were removed. These erroneous duplications are due to a bug in the script used to extract 12S rRNA gene sequences from mitogenome annotations. Note that four mitogenome records (AP005998, KJ643927, NC_024573, OP326524) in the May2023 release contain 2 copies of the 12S rRNA gene. These were presented as separate entries sharing the same accession number in mitofish.12S.May2023.tsv.

Major update (Nov2022): The 12S rRNA gene sequence dataset is now filtered to only contain mitochondrial genomes annotated with 12S rRNA gene sequences. Sequences of the 12S rRNA gene are now extracted from complete mitochondrial genomes to construct a more gene-specific 12S rRNA dataset. 12S rRNA gene sequences in mitohelper's dataset are available for download as mitofish.12S.$month$year_NR.fasta

Mitohelper is a repository built to facilitate experimental design, alignment visualization, and reference sequence analysis in fish eDNA studies. Refer to our paper and Mitohelper's wiki for database construction pipeline.

I. Reference database files in tab-separated format, containing gene, taxonomy, and sequence information:

• mitofish.all.May2023.tsv (809,533 records)
• mitofish.12S.May2023.tsv (48,076 records)
• mitofish.12S.May2023_NR.fasta (fasta file of 12S rRNA gene records)
• mitofish.COI.May2023.tsv (329,730 records)

II. De-replicated QIIME 2-compatible 12S/12S+16S+18S rRNA reference datasets:

• 12S-seqs-derep-uniq.qza 
• 12S-tax-derep-uniq.qza 
• 12S-16S-18S-seqs.qza 
• 12S-16S-18S-tax.qza 

If you use Mitohelper, please cite:
Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1– 10.  https://doi.org/10.1002/edn3.187