Nozomu Iwasaki

Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): notable differences in gene arrangement.

Precious coral are taxonomically a group of corals that belong to the family Coralliidae within the order Alcyonacea, subclass Octocorallia, and class Anthozoa, whose skeletal axes are used for jewelry. They are distributed in the Mediterranean Sea and in waters adjacent to Japan, Taiwan, Midway Island and the Hawaiian Islands. The genus Corallium of the family Coralliidae was recently divided into two genera, Corallium and Paracorallium, based on morphological observations, but insufficient molecular evidence to support this classification has been presented to date. We determined for the first time the complete mitochondrial genome sequence of two precious corals P. japonicum and C. konojoi, in order to clarify their systematic positions. The circular mitochondrial genomes of P. japonicum and C. konojoi are 18,913bp and 18,969bp in length, respectively, and encode 13 typical energy pathway protein coding genes (nad1-6, nad4L, cox1-3, cob, atp6 and atp8), two ribosomal RNA genes (rns and rnl), a transfer RNA (trnM) and a mismatch repair gene homologue msh1. The two genomes have an overall nucleotide sequence identity of 97.5%, which is comparable to that between Acanella eburnea and Keratoisidinae sp. belonging to Octocorallia. Surprisingly, however, their gene arrangements were not identical. Phylogenetic analyses using seven complete mitochondrial genome sequences belonging to species in the subclass Octocorallia indicated that within the subclass, at least three gene order rearrangement events occurred during evolution. Our results support the validity of the morphological classification that separated the family Coralliidae into two genera, Corallium and Paracorallium.

Identification of the chemical form of sulfur compounds in the Japanese pink coral (Corallium elatius) skeleton using μ-XRF/XAS speciation mapping

The distributions and chemical forms of sulfur compounds in the skeleton of Japanese pink coral (Corallium elatius) were investigated using X-ray spectroscopic techniques combined with micro-focused soft X-ray radiation. Microscopic X-ray fluorescence/soft X-ray photoabsorption (μ-XRF/XAS) speciation mapping clarified that sulfate is the primary species in the coral skeleton, with minor amounts of organic sulfur, whereas both sulfate and organic sulfur coexist in coenenchyme. Analysis of the post-edge region of the XAS spectra confirmed that sulfate ions in the coral skeleton are mainly in the form of gypsum-like inorganic sulfate substituting for the carbonate ions in the calcite skeleton. The sulfate concentration was negatively correlated with the magnesium concentration and positively correlated with that of phosphorus. Speciation mapping of sulfate in the coral skeleton showed clear fluctuations with sulfate concentrations being higher at dark bands, whereas the small amount of organic sulfur had unclear dark/bright bands. These results suggest that the little organic sulfur that is present is contained in the organic matter embedded in the biocrystal of coral skeleton.

Morphometry and population structure of non-harvested and harvested populations of the Japanese red coral (Paracorallium japonicum) off Amami Island, southern Japan

Precious coral harvested in the Mediterranean Sea and the northern Pacific Ocean is of commercial value yet excessive fishing has led to a serious decline in its abundance. Consequently, there is now international discussion about controlling the world trade of precious coral. To explore the possibility of a sustainable fishery of Japanese red coral (Paracorallium japonicum), the morphometry and the population structure of populations in a non-harvested area and in a harvested area were investigated using a remotely operated vehicle (ROV) off Amami Island, Southern Japan, in 2009. In the harvested population, the estimated modal ages are 10 to 20 years. In contrast, the main mode in the non-harvested population extends widely from 20 to 40 years, with a small but distinct secondary mode between 50 and 60 years. Commercially collected specimens are mainly 30–40 years old. The difference in the modes of non-harvested and harvested populations suggests that harvested populations return to the pre-fishing level after at least 10–20 years of a biological rest period. This study indicates a rotational harvest is useful for sustainable management.

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry. The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969-18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1-6, nad4L, cox1-3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.

Magnesium K-edge XANES spectroscopy of geological standards

Magnesium K-edge X-ray absorption near-edge structure (XANES) spectra have been investigated to develop a systematic understanding of a suite of Mg-bearing geological materials such as silicate and carbonate minerals, sediments, rocks and chemical reagents. For the model compounds the Mg XANES was found to vary widely between compounds and to provide a fingerprint for the form of Mg involved in geologic materials. The energy positions and resonance features obtained from these spectra can be used to specify the dominant molecular host site of Mg, thus shedding light on Mg partitioning and isotope fractionation in geologic materials and providing a valuable complement to existing knowledge of Mg geochemistry.

Redescription of Alectona verticillata (Johnson) (Porifera, Alectonidae) boring into Japanese precious coral

Abstract The boring sponge Alectona (Nisella) verticillata (Johnson, 1899) was recorded, for the first time after the description, in a colony of Corallium elatius collected in the south of the Ryukyu Islands (Japan Sea). The material recorded allowed a redescription of the species based on the SEM analyses of its spicular complement. Alectona verticillata is the only species of the genus characterised by three kinds of amphiasters and by the lack of the large, spiny or tubercolate diactines, considered typical of the genus. Its distribution recalls the Tethyan distribution of the genus Corallium, indicating a high specificity of boring sponges for their substrata.

Notable diversity in hemoglobin expression patterns among species of the deep-sea clam, Calyptogena

The deep-sea clams Calyptogena nautilei and C. tsubasa, which live in the cold-seep area at a depth of 3570 m in the Nankai Trough, Japan, have abundant hemoglobins (Hbs) in erythrocytes, similar to other Calyptogena species. We determined the cDNA-derived amino acid sequences of Hbs from two Calyptogena species. C. tsubasa was found to contain two dimeric Hbs, Hb I consisting of 145 amino acid residues and Hb II with 137 residues, similar to known Hbs from C. soyoae and C. kaikoi. Sequence identity was over 90% among the orthologous chains of Calyptogena Hbs. On the other hand, surprisingly, C. nautilei contained two monomeric Hbs, Hb III containing 141 residues and Hb IV with 134 residues. In addition, Hbs III and IV showed only 33–42% sequence identity with Hbs I and II from other Calyptogena species. The distal (E7) histidine, one of the functionally important residues of the heme protein, is replaced by glutamine in all Hb chains of Calyptogena species. A phylogenetic analysis indicated that C. nautilei Hb III is closer to Hb I from other Calyptogena species. We suppose that a Hb gene was duplicated at least three times in an immediate ancestor of Calyptogena and, presumably depending on physiological conditions different Hb sets are being expressed: dimeric Hbs I and II in C. soyoae, C. kaikoi and C. tsubasa, and monomeric Hbs III and IV in C. nautilei.

A new species ofSergia from the Red Sea (Crustacea: Decapoda: Sergestidae)

Sergia erythraeensis sp. nov., a sergestid shrimp, is described. The species is apparently endemic to the Red Sea.KurzfassungSergia erythraeensis sp. nov., eine neue Sergestiden-Art, die anscheinend endemisch für das Rote Meer ist, wird beschrieben.

Arginine kinases from the marine feather star Tropiometra afra macrodiscus: The first finding of a prenylation signal sequence in metazoan phosphagen kinases

Two arginine kinase cDNAs (AK1 and AK2) were isolated from the marine feather star Tropiometra afra macrodiscus, and the gene structure (exon/intron organization) of AK1 was determined. The cDNA-derived amino acid sequences and the exon/intron organization of the Tropiometra AK1 gene were homologous to those of a human creatine kinase (CK) as well as the AK of the sea cucumber Stichopus. Phylogenetic analysis also supports the close relationship between human CKs and echinoderm AKs, indicating that the latter AKs evolved from an ancestral CK gene. We observed that the Tropiometra AK1 gene has a novel C-terminal extension (approximately 50 amino acid residues) encoded by a unique exon. Moreover, a typical prenylation signal sequence (CSLL) was found at the C-terminal end of this extension, suggesting that AK1 is anchored to a membrane. AK2 had no such C-terminal extension. This is the first finding of a prenylation signal in metazoan phosphagen kinases. Recombinant Tropiometra AK1 and AK2 enzymes were successfully expressed in Escherichia coli, and their kinetic constants were determined. Both enzymes showed activity comparable to that of typical invertebrate AKs.

A new species of Thoosa (Demospongiae, Hadromerida) excavating precious coral Corallium sp. from Midway

A new species of Thoosa, T. midwayi n. sp., excavating the scleraxis of Corallium sp. and collected in the Midway Islands, is described on the basis of its spicular complement characterised by two types of amphiasters. The new species differs from the closest species, T. amphiasterina Topsent, in the shape and size of the amphiasters. Although still at a very initial stage, the study of the sponges boring into the scleraxis of Pacific precious corals suggests that the boring assemblage varies according to the different coral populations probably due to the different species of the genus Corallium present in the Pacific area and to the geographical isolation of the precious coral banks.