Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples

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. Design Type(s) database creation objective • data integration objective Measurement Type(s) Taxonomy Technology Type(s) digital curation Factor Type(s) gene list Sample Characteristic(s) Metazoa Design Type(s) database creation objective • data integration objective Measurement Type(s) Taxonomy Technology Type(s) digital curation Factor Type(s) gene list Sample Characteristic(s) Metazoa Machine-accessible metadata file describing the reported data (ISA-Tab format)

• Publication year

  2017

• Venue

  Scientific Data

• Publication date

  2017-03-14

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/sdata.2017.27PMID 28291235PMCID 5349245
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Censusing marine eukaryotic diversity in the twenty-first century

  2016cited by this paper
• SPINGO: a rapid species-classifier for microbial amplicon sequences

  2015cited by this paper
• DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

  2015cited by this paper
• A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

  2013cited by this paper
• Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

  2012cited by this paper
• Sequencing our way towards understanding global eukaryotic biodiversity.

  2012cited by this paper
• PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

  2012cited by this paper
• PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences

  2012cited by this paper
• The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

  2012cited by this paper
• The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

  2012cited by this paper
• Memory, Visual Discrimination Performance, and the Human Hippocampus

  2011cited by this paper
• Second-generation environmental sequencing unmasks marine metazoan biodiversity

  2010cited by this paper
• BLAST+: architecture and applications

  2009cited by this paper
• Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

  2008cited by this paper
• Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

  2007cited by this paper
• Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

  1991cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

  1989cited by this paper
• Rapid evolution of animal mitochondrial DNA.

  1979cited by this paper

• Benthic foraging and regional dietary variations of yellowtail (Seriola quinqueradiata) at their northern range limit revealed by integrated stomach content and DNA metabarcoding analyses

  2026cites this paper
• A Regional DNA Barcode Library for Northern Rocky Mountain Arthropods to Support Biodiversity and Molecular Ecological Research.

  2026cites this paper
• A long-term ecological research dataset from the marine genetic monitoring programme ARMS-MBON 2020-2021

  2025cites this paper
• Geographic variation in diet, prey resources and exposure to parasites and saxitoxin in Steller sea lions in the Gulf of Alaska

  2025cites this paper
• Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding

  2025cites this paper
• Chemical, biochemical and environmental DNA analysis of sediments from two seamounts of the deep Arabian Sea

  2025cites this paper
• Unraveling multipredator impacts in salmon‐bearing rivers using quantitative DNA metabarcoding

  2025cites this paper
• Gaps and Data Ambiguities in DNA Reference Libraries: A Limiting Factor for Molecular‐Based Biodiversity Assessments Using Annelids as a Case Study

  2025cites this paper
• DNA Metabarcoding of Macroinvertebrates in the Biomonitoring System of Lake Baikal

  2025cites this paper
• Omics exploration of deep-sea biodiversity: data from the “Pourquoi Pas les Abysses?” and eDNAbyss projects

  2025cites this paper
• Using iDNA to determine impacts of Amazonian deforestation on Leishmania hosts, vectors, and their interactions

  2025cites this paper
• Evaluating DNA extraction methods for eDNA metabarcoding of soil invertebrate diversity

  2025cites this paper
• A review of autonomous reef monitoring structures (ARMS) for monitoring hard‐bottom benthic biodiversity

  2025cites this paper
• Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas.

  2024cites this paper
• DNA barcoding reference libraries of Italian Plecoptera: a gap analysis

  2024cites this paper
• Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan

  2024cites this paper
• A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020

  2024cites this paper
• Ecosystem transplant from a healthy reef boosts coral health at a degraded reef

  2024cites this paper
• Benchmarking the discrimination power of commonly used markers and amplicons in marine fish (e)DNA (meta)barcoding

  2024cites this paper
• Diet of non-breeding leach’s storm-petrels (Hydrobates leucorhous) in the sub-polar frontal zone of the North Atlantic

  2024cites this paper
• Unveiling the Faunal Diversity in the Water Column Adjacent to Two Seamounts in the Deep Arabian Sea Using Environmental DNA Metabarcoding

  2024cites this paper
• Dietary resilience of coral reef fishes to habitat degradation

  2024cites this paper
• An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

  2024cites this paper
• Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

  2024influential citation
• MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.

  2024cites this paper
• Citizen science approach for genetic species identification in a local French seafood speciality

  2024cites this paper
• Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula

  2024cites this paper
• Interdisciplinary approaches at early invasion stages maximise the evidence on human-induced and climate-driven fish dispersal

  2024cites this paper
• The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

  2023cites this paper
• DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler

  2023cites this paper
• BEE‐quest of the nest: A novel method for eDNA‐based, nonlethal detection of cavity‐nesting hymenopterans and other arthropods

  2023cites this paper
• Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics

  2023cites this paper
• Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River.

  2023cites this paper
• Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries

  2023cites this paper
• A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding

  2023cites this paper
• Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand

  2023cites this paper
• Exploring New Frontiers in Coral Nurseries: Leveraging 3D Printing Technology to Benefit Coral Growth and Survival

  2023cites this paper
• An automated workflow to assess completeness and curate GenBank for environmental DNA metabarcoding: The marine fish assemblage as case study

  2023cites this paper
• The Genus Heterogynis Rambur, 1866 (Heterogynidae, Lepidoptera): Congruence of Molecular, Morphological and Morphometric Evidence Reveal New Species in Serbia

  2023cites this paper
• Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding

  2023cites this paper
• Nematode mitochondrial metagenomics: A new tool for biodiversity analysis

  2023cites this paper
• Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions

  2023cites this paper
• COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline

  2023cites this paper
• Measuring protected-area effectiveness using vertebrate distributions from leech iDNA

  2022cites this paper
• Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

  2022cites this paper
• Measuring protected-area effectiveness using vertebrate distributions from leech iDNA

  2022cites this paper
• Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects—A proof of concept from the field

  2022cites this paper
• General principles for assignments of communities from eDNA : Open versus closed taxonomic databases

  2022cites this paper
• An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

  2022cites this paper
• Nanopore short‐read sequencing: A quick, cost‐effective and accurate method for DNA metabarcoding

  2022cites this paper
• Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes

  2022cites this paper
• An automated workflow to assess completeness and curate GenBank for eDNA metabarcoding: the marine fish assemblage as case study

  2022cites this paper
• Net overboard: Comparing marine eDNA sampling methodologies at sea to unravel marine biodiversity

  2022cites this paper
• Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

  2022cites this paper
• Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding.

  2022cites this paper
• Dietary diversity of multiple shorebird species in an Asian subtropical wetland unveiled by DNA metabarcoding

  2022cites this paper
• MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences

  2022cites this paper
• Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems

  2022cites this paper
• Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins

  2022influential citation
• Revealing the foraging movements and diet of the White-faced Storm Petrel Pelagodroma marina in the NE Atlantic

  2022cites this paper
• Seq’ and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

  2022influential citation
• Development of transcriptomics‐based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets

  2022cites this paper
• Next Generation Sequencing-based DNA metabarcoding for animal species profiling in fish feed

  2022cites this paper
• Metatranscriptomics reveals higher species compositional homogeneity in smaller size coral reef zooplankton

  2022cites this paper
• Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies

  2022cites this paper
• Spider webs as eDNA samplers: Biodiversity assessment across the tree of life

  2022influential citation
• Feces DNA analyses track the rehabilitation of a free-ranging beluga whale

  2022cites this paper
• MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

  2022cites this paper
• Ignacio Ribera´s Tree of Life

  2022cites this paper
• Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity

  2021cites this paper
• Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests

  2021cites this paper
• PIMBA: a PIpeline for MetaBarcoding Analysis

  2021cites this paper
• Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

  2021influential citation
• Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

  2021cites this paper
• Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

  2021cites this paper
• Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies

  2021cites this paper
• Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

  2021influential citation
• Detection of Macrobenthos Species With Metabarcoding Is Consistent in Bulk DNA but Dependent on Body Size and Sclerotization in eDNA From the Ethanol Preservative

  2021cites this paper
• The Study of the Diversity of Hydrobionts from Listvennichny Bay of Lake Baikal by DNA Metabarcoding

  2021cites this paper
• Recommendations for interpreting zooplankton metabarcoding and integrating molecular methods with morphological analyses

  2021cites this paper
• Bacteria are everywhere, even in your COI marker gene data!

  2021cites this paper
• Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes.

  2021cites this paper
• Patterns Based on Molecular ’ The role of taxonomic expertise in interpretation of metabarcoding studies

  2021cites this paper
• Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey

  2021influential citation
• DNA metabarcoding reveals the dietary composition in the endangered black-faced spoonbill

  2021cites this paper
• Using metatranscriptomics to estimate the diversity and composition of zooplankton communities

  2021influential citation
• Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications

  2021cites this paper
• DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review

  2021cites this paper
• Development of transcriptomics-based eukaryotes growth rate indices

  2021cites this paper
• Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach

  2021cites this paper
• The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

  2021cites this paper
• The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures

  2021cites this paper
• New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches

  2021cites this paper
• Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA

  2020cites this paper
• DNA metabarcoding provides insights into the diverse diet of a dominant suspension feeder, the giant plumose anemone Metridium farcimen

  2020cites this paper
• CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis

  2020cites this paper
• Reply to Locatelli et al.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts’ effort in each group

  2020cites this paper
• Measuring protected-area outcomes with leech iDNA: large-scale quantification of vertebrate biodiversity in Ailaoshan reserve

  2020cites this paper
• Environmental DNA for tracking waterhole visitation in savanna ecosystems

  2020cites this paper
• Metabarcoding as a tool to enhance marine surveillance of nonindigenous species in tropical harbors: A case study in Tahiti

  2020cites this paper