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Shinjuku, Japan

Yamanoue Y.,University of Tokyo | Setiamarga D.H.E.,University of California at San Diego | Matsuura K.,Collection Center
Journal of Fish Biology | Year: 2010

The pelvic fins of teleosts are paired appendages that are considered to be homologous to the hind limbs of tetrapods. Because they are less important for swimming, their morphology and function can be flexibly modified, and such modifications have probably facilitated the adaptations of teleosts to various environments. Recently, among these modifications, pelvic-fin loss has gained attention in evolutionary developmental biology. Pelvic-fin loss, however, has only been investigated in a few model species, and various biological aspects of pelvic fins in teleosts in general remain poorly understood. This review summarizes the current state of knowledge regarding pelvic fins, such as their structure, function and evolution, to elucidate their contribution to the considerable diversity of teleosts. This information could be invaluable for future investigations into various aspects of pelvic fins, which will provide clues to understanding the evolution, diversity and adaptations of teleosts. © 2010 The Fisheries Society of the British Isles.

Campbell M.A.,Massey University | Lopez J.A.,University of Alaska Fairbanks | Satoh T.P.,Collection Center | Chen W.-J.,National Taiwan University | Miya M.,Natural History Museum and Institute
Gene | Year: 2014

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data. © 2014 Elsevier B.V.All rights reserved.

Satoh T.P.,Collection Center | Sato Y.,National Institute of Genetics | Masuyama N.,University of Tokyo | Masuyama N.,Resonarch Co. | And 2 more authors.
BMC Genomics | Year: 2010

Background: Mitochondrial (mt) gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years. It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order.Results: Based on the analysis of codon usage and tRNA gene positions, we suggest that tRNA gene order of the typical vertebrate mt-genomes may be important for their translational efficiency. The vertebrate mt-genome encodes 2 rRNA, 22 tRNA, and 13 transmembrane proteins consisting mainly of hydrophobic domains. We found that the tRNA genes specifying the hydrophobic residues were positioned close to the control region (CR), where the transcription efficiency is estimated to be relatively high. Using 47 vertebrate mt-genome sequences representing jawless fishes to mammals, we further found a correlation between codon usage and tRNA gene positions, implying that highly-used tRNA genes are located close to the CR. In addition, an analysis considering the asymmetric nature of mtDNA replication suggested that the tRNA loci that remain in single-strand for a longer time tend to have more guanine and thymine not suffering deamination mutations in their anticodon sites.Conclusions: Our analyses imply the existence of translational constraint acting on the vertebrate mt-gene arrangement. Such translational constraint, together with the deamination-related constraint, may have contributed to long-term maintenance of gene order. © 2010 Satoh et al; licensee BioMed Central Ltd.

Coccato A.,Ghent University | Karampelas S.,Gubelin Gem Laboratory | Worle M.,Collection Center | Van Willigend S.,Swiss National Museum | Petrequin P.,University of Franche Comte
Journal of Raman Spectroscopy | Year: 2014

Raman spectroscopy was used for the characterization of seven gem quality green 'jade' samples and three green 'jade' samples of archaeological importance. The results were also compared with those acquired by other nondestructive techniques such as classical gemology, energy-dispersive X-ray fluorescence (EDXRF), ultraviolet-visible-near infrared (UV-Vis-NIR) in absorption, Fourier transform infrared spectroscopy (FTIR) in absorption and micro-FTIR in reflectance. Five samples of gem quality and two samples of archaeological interest were found to be 'jadeite jade', whereas two samples of gem quality and one sample of archaeological interest were 'omphacite jade'. Raman spectroscopy is found to be the most efficient method for their characterization. The results were confirmed with EDXRF and micro-FTIR in reflectance. Data acquired using classical gemology, UV-Vis-NIR absorption and FTIR absorption spectroscopy were similar on 'omphacite jade' and 'jadeite jade'. Copyright © 2014 John Wiley & Sons, Ltd.

Iwasaki W.,University of Tokyo | Fukunaga T.,University of Tokyo | Isagozawa R.,University of Tokyo | Yamada K.,RNAi Company Ltd | And 7 more authors.
Molecular Biology and Evolution | Year: 2013

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. © The Author 2013.

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