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MitoFish specifications


Unique identifier OMICS_22427
Name MitoFish
Alternative name Mitochondrial Genome Database of Fish
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 3.29
Maintained Yes


  • person_outline Wataru Iwasaki
  • person_outline Mutsumi Nishida

Publication for Mitochondrial Genome Database of Fish

MitoFish citations


Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance

Sci Rep
PMCID: 5807545
PMID: 29426945
DOI: 10.1038/s41598-018-20946-5
call_split See protocol

[…] The complete mitogenome sequence data was assembled and analyzed using Seqman program of Lasergene software. Mitochondrial DNA annotation was done using Mitos WebServer and MitoFish. MitoAnnotator was used to generate a gene map of complete mitogenome of M. indica. Careful manual annotation was conducted using the Artemis software with the help of BLAST, for ensuring the […]


Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

Sci Rep
PMCID: 5681689
PMID: 29127415
DOI: 10.1038/s41598-017-15702-0
call_split See protocol

[…] gun assembly were compared. If they were identical, that meaning this method was precise. Moreover, the PCGs, rRNA genes, tRNA genes and D-loop region of mtDNA were annotated by MitoAnnotator ( with parameters of complete circular genome. The mtDNA sequence of C. umbratile has been deposited in the GenBank database under accession numbers KX […]


Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific

PLoS One
PMCID: 5533319
PMID: 28753660
DOI: 10.1371/journal.pone.0181329
call_split See protocol

[…] IS version 3.2 (Hitachi Software Engineering, Yokohama, Japan) were used to concatenate the consensus mitogenomic sequence.The consensus sequences were annotated using the pipeline "MitoAnnotator" of MitoFish [] and then exported for analyses. The gene content and order of the newly determined mitogenomic sequences were typical of those found in most other teleosts []. provides information on the […]


Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

BMC Genomics
PMCID: 5418769
PMID: 28472937
DOI: 10.1186/s12864-017-3709-3

[…] tRNA regions due to the punctuation pattern of the mitochondrial transcript expression. These gaps were filled with Ns.The assembled mitochondrial genomes were annotated using the web-based services MitoFish and MITOS [, ], and manually curated for inconsistencies. To estimate the sequencing depth of each base, Bowtie v. 1.0.0 was used to align Illumina reads onto the assembled mitogenomes. Align […]


The complete mitochondrial genome of the threatened Neotropical catfish Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae) and phylogenomic analysis indicate monophyly of Pimelodoidea

Genet Mol Biol
PMCID: 5127154
PMID: 27648766
DOI: 10.1590/1678-4685-GMB-2016-0007

[…] ial mitogenome assembly generated by MIRA was used as an input for the MITObim algorithm () using default parameters. Mitogenome coverage was obtained using Tablet software (). Mitos WebServer () and MitoFish () were used for annotation. Blast searches () against fish amino acid sequences confirmed gene boundaries. tRNA predictions were confirmed using tRNAscan-SE (). Ribosomal RNA annotations wer […]


Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus

Front Physiol
PMCID: 5005410
PMID: 27630577
DOI: 10.3389/fphys.2016.00379

[…] Complete mitochondrial genomes from several other Cyprinodontiform fishes were retrieved from the MitoFish database for comparative analysis (Table ; Iwasaki et al., ). Mitochondrial genes in comparator species were identified using the MitoAnnotator pipeline as done with A. limnaeus. Individual c […]


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MitoFish institution(s)
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan; Department of Computational Biology, The University of Tokyo, Chiba, Japan; RNAi Incorporated, Tokyo, Japan; Collection Center, National Museum of Nature and Science, Ibaraki, Japan; Department of Zoology, Natural History Museum and Institute, Chiba, Japan
MitoFish funding source(s)
Supported by the Japan Society for the Promotion of Science (Grant Numbers 13556028, 19207007, 23370041, 23710231, 178087, 248046, and 258048) and the Japan Science and Technology Agency (CREST).

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