Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment …

T Jo, K Takao, T Minamoto - Environmental DNA, 2022 - Wiley Online Library
Environmental DNA (eDNA) analysis is a revolutionary tool for non‐invasive, cost‐effective,
and highly sensitive monitoring of species distribution and abundance; however, there …

Marine invasive alien species in Europe: 9 years after the IAS Regulation

S Katsanevakis, S Olenin, R Puntila-Dodd… - Frontiers in Marine …, 2023 - frontiersin.org
Biological invasions, resulting from human activities, exert substantial impacts on
ecosystems worldwide. This review focuses on marine invasive alien species (IAS) in …

OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes

S Greiner, P Lehwark, R Bock - Nucleic acids research, 2019 - academic.oup.com
Organellar (plastid and mitochondrial) genomes play an important role in resolving
phylogenetic relationships, and next-generation sequencing technologies have led to a …

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

G Meng, Y Li, C Yang, S Liu - Nucleic acids research, 2019 - academic.oup.com
Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological
studies. It becomes routine to utilize multiple genes on mitogenome or the entire …

Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

A Donath, F Jühling, M Al-Arab… - Nucleic acids …, 2019 - academic.oup.com
With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual
annotation is becoming more and more infeasible. While it is easy to identify the …

Non‐specific amplification compromises environmental DNA metabarcoding with COI

RA Collins, J Bakker, OS Wangensteen… - Methods in Ecology …, 2019 - Wiley Online Library
Metabarcoding extra‐organismal DNA from environmental samples is now a key technique
in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when …

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

M Miya, Y Sato, T Fukunaga, T Sado… - Royal Society …, 2015 - royalsocietypublishing.org
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding
environmental DNA (eDNA) from fishes. Primers were designed using aligned whole …

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

S Yamamoto, R Masuda, Y Sato, T Sado, H Araki… - Scientific reports, 2017 - nature.com
Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to
assess aquatic community structures. However, the method has hitherto lacked field tests …

MitoFish, MitoAnnotator, and MiFish Pipeline: updates in 10 years

T Zhu, Y Sato, T Sado, M Miya… - Molecular Biology and …, 2023 - academic.oup.com
Abstract MitoFish, MitoAnnotator, and MiFish Pipeline are comprehensive databases of fish
mitochondrial genomes (mitogenomes), accurate annotation software of fish mitogenomes …

Structure and variation of the mitochondrial genome of fishes

TP Satoh, M Miya, K Mabuchi, M Nishida - BMC genomics, 2016 - Springer
Background The mitochondrial (mt) genome has been used as an effective tool for
phylogenetic and population genetic analyses in vertebrates. However, the structure and …