TY - JOUR
T1 - MitoFish and mifish pipeline
T2 - A mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding
AU - Sato, Yukuto
AU - Miya, Masaki
AU - Fukunaga, Tsukasa
AU - Sado, Tetsuya
AU - Iwasaki, Wataru
N1 - Funding Information:
The authors thank Mutsumi Nishida, Koichiro Yamada, Takashi P. Satoh, Ryota Isagozawa, Yasunobu Maeda, Kohji Mabuchi, and Hirohiko Takeshima for their help in the development of MitoFish. This work was supported by the Japan Science and Technology Agency (CREST), the Japan Society for the Promotion of Science (Grant Numbers 15K18590, 16H06279, 17K19298, and 17HP8031), the University of the Ryukyus (the Spatiotemporal Genomics Project), and the Canon Foundation. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics. Sequence data are deposited in DDBJ Sequence Read Archive with an accession number DRA006629.
Publisher Copyright:
© The Author(s) 2018.
PY - 2018/6
Y1 - 2018/6
N2 - Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at http://mitofish.aori.u-Tokyo.ac.jp/ (last accessed April 7th, 2018).
AB - Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at http://mitofish.aori.u-Tokyo.ac.jp/ (last accessed April 7th, 2018).
KW - Database
KW - Environmental DNA
KW - Fish
KW - Metabarcoding
KW - Mitochondrial genome
UR - http://www.scopus.com/inward/record.url?scp=85051927286&partnerID=8YFLogxK
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U2 - 10.1093/molbev/msy074
DO - 10.1093/molbev/msy074
M3 - Article
C2 - 29668970
AN - SCOPUS:85051927286
SN - 0737-4038
VL - 35
SP - 1553
EP - 1555
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 6
ER -