Data from: 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.