MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline
Wataru Iwasaki,Tsukasa Fukunaga,Ryota Isagozawa,Koichiro Yamada,Yasunobu Maeda,Takashi P. Satoh,Tetsuya Sado,Kohji Mabuchi,Hirohiko Takeshima,Masaki Miya,Mutsumi Nishida +10 more
TLDR
MitoFish contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses.Abstract:
Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.read more
Citations
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Journal ArticleDOI
OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.
TL;DR: A new version of OGDRAW equipped with a new front end enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades.
Journal ArticleDOI
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
Masaki Miya,Yukuto Sato,Tsukasa Fukunaga,Tetsuya Sado,J. Y. Poulsen,Keiichi Sato,Toshifumi Minamoto,Satoshi Yamamoto,Hiroki Yamanaka,Hitoshi Araki,Michio Kondoh,Wataru Iwasaki +11 more
TL;DR: The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods and has the potential to serve as an alternative tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Journal ArticleDOI
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.
TL;DR: A mitogenome toolkit MitoZ is developed, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenomes assembly together with annotations and visualization results from HTS raw reads.
Journal ArticleDOI
Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea
Satoshi Yamamoto,Reiji Masuda,Yukuto Sato,Tetsuya Sado,Hitoshi Araki,Michio Kondoh,Toshifumi Minamoto,Masaki Miya +7 more
TL;DR: The ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters by using high-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km2 revealed the fish community structure at a species resolution.
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