ArticleScientific data2017
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples.
Article in Scientific data, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 202 citations in OpenAlex.
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- A long-term ecological research dataset from the marine genetic monitoring programme ARMS-MBON 2020-2021.Biodiversity data journal · 2025Article
- Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding.PloS one · 2025Article
- Ecosystem transplant from a healthy reef boosts coral health at a degraded reef.Nature communications · 2024Article
- Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries.Current zoology · 2024Article
- An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding.Nature communications · 2024Article
- Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula.Scientific reports · 2024Article
- Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan.Biodiversity data journal · 2024Article
- Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand.Scientific reports · 2023Article
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- Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient.Scientific reports · 2022Article
- Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets.Molecular ecology resources · 2022Article
- Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins.Database : the journal of biological databases and curation · 2022Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water). Yet, unlike nuclear ribosomal RNA markers, there is to date no high-quality reference dataset available for taxonomic assignments. Here, we retrieved all metazoan mitochondrial gene sequences from GenBank, and then quality filtered and formatted the datasets for taxonomic assignments using taxonomic assignment tools. The reference datasets-'Midori references'-are available for download at www.reference-midori.info. Two versions are provided: (I) Midori-UNIQUE that contains all unique haplotypes associated with each species and (II) Midori-LONGEST that contains a single sequence, the longest, for each species. Overall, the mitochondrial Cytochrome oxidase subunit I gene was the most sequence-rich gene. However, sequences of the mitochondrial large ribosomal subunit RNA and Cytochrome b apoenzyme genes were observed for a large number of species in some phyla. The Midori reference is compatible with some taxonomic assignment software. Therefore, automated high-throughput sequence taxonomic assignments can be particularly effective using these datasets.
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