title: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples.
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.
authors.affiliation: Biodiversity Research Centre, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Ryuji J
authors.initials: RJ
authors.lastname: Machida
authors.affiliation: Smithsonian Tropical Research Institute, Panama City, Republic of Panama.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Leray
authors.affiliation: Biodiversity Research Centre, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Shian-Lei
authors.initials: SL
authors.lastname: Ho
authors.affiliation: National Museum of Natural History, Smithsonian Institution, Washington DC 20560-0163, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Knowlton
mesh_terms: D000818:Animals; D050259:Genes, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D012984:Software