Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones,Isolated from Malaysian Tropical Soil

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.     

Entomopathogenic Nematodes for Biological Control of Pryeria sinica Moore (Lepidoptera: Zygaenidae) and Persistence on Euonymus japonica Thunberg Foliage

Korean entomopathogenic nematodes (EPN), Steinernema carpocapsae Pocheon strain, Steinernema sp. GSNUS-4 strain, Steinernema sp. GSNUS-14 strain, Steinernema sp. GSNUS-16 strain, Heterorhabditis sp. GSNUH-2 strain, and Heterorhabditis sp. GSNUH-3 strain were evaluated for the biological control of pellucid zygaenid, Pryeria sinica Moore (Lepidoptera: Zygaenidae), a leaf-feeding insect pest of Euonymus japonica Thunberg. In addition, persistence of S. carpocapsae Pocheon strain on E. japonica foliage was checked.Nematode species, strain, and concentration influenced infectivity of Korean EPNs against 3rd instar of P. sinica larvae. S. carpocapsae Pocheon strain was the most effective nematode.Larval mortality by S. carpocapsae Pocheon strain in the exposure experiments was low in both light and dark conditions representing 36.7% at 100 infective juveniles/larva in each dark and light condition. Mortality by fenitrothion, however, was 100% 3 days later. Infectivity of S. carpocapsae Pocheon strain was not different between non-exposed foliage and exposed foliage to sunlight for 30 min.Mortality of 4th instar of P. sinica larvae was very low for both S. carpocapsae Pocheon alone and S carpocapsae Pocheon with spreading agent. Application time of nematodes, shading, and leaf position on the tree influenced persistence of S. carpocapsae Pocheon strain on E. japonica foliage. Nematode survival on foliage was positively correlated with shading level and higher at the lowest level than the middle or upper level of the tree.     

Strain selection and initiation timing influence the cultivation period of <Emphasis Type="Italic">Saccharina japonica</Emphasis> and their impact on the abalone feed industry in Korea

Cultivations of the brown seaweed, Saccharina japonica, was developed, promoted, and industrialized in the 1970s and is highly valued in Korea both for human consumption and as a feed for the rapidly developing abalone farming industry. Production has continually increased, and approximately 442,637 tonnes wet weight was harvested in Korea in 2015. Abalone is a highly sought-after delicacy in Korea, and the abalone farming industry has been developed based on a stable production of seaweed. Korean abalone farmers prefer to feed their stock on locally cultured S. japonica; however, between August and November, the supply of farmed S. japonica declines because higher seawater temperatures reduce S. japonica productivity. In an attempt to overcome this temperature-induced period of low production, cultivation trials with a strain of S. japonica selected to withstand higher cultivation temperatures were undertaken. Strain selection involved using individual parent thalli that were found to remain productive under high seawater temperature (26 °C) at Wando. Male and female gametophytes were isolated through 3 cycles of free-living gametophyte culture to produce the F₃ strain used in the production trials. Production trials using the selected strain were initiated every month between December 2014 and March 2015. This delayed the initiation of culture beyond the latest initiation time currently used by farmers (December). Delaying initiation of cultivation resulted in delayed maximum growth compared to the control. Growth of the F₃ strain continued for up to 3 months longer than normally achieved on farms for non-selected thalli. The mean length, growth rate, and biomass were also greater than those achieved by the control strain. The use of the F₃ strain of S. japonica coupled with delayed initiation of culture can therefore be used to help to ensure a stable year round algal feed supply for abalone industry in Korea.     

The utility of Shewanella japonica for microbial fuel cells

Shewanella-containing microbial fuel cells (MFCs) typically use the fresh water wild-type strain Shewanella oneidensis MR-1 due to its metabolic diversity and facultative oxidant tolerance. However, S. oneidensis MR-1 is not capable of metabolizing polysaccharides for extracellular electron transfer. The applicability of Shewanella japonica (an agar-lytic Shewanella strain) for power applications was analyzed using a diverse array of carbon sources for current generation from MFCs, cellular physiological responses at an electrode surface, biofilm formation, and the presence of soluble extracellular mediators for electron transfer to carbon electrodes. Critically, air-exposed S. japonica utilizes biosynthesized extracellular mediators for electron transfer to carbon electrodes with sucrose as the sole carbon source.     

Bacteria Endosymbiont,Wolbachia, Promotes Parasitism of Parasitoid Wasp Asobara japonica

Wolbachia is the most widespread endosymbiotic bacterium that manipulates reproduction of its arthropod hosts to enhance its own spread throughout host populations. Infection with Wolbachia causes complete parthenogenetic reproduction in many Hymenoptera, producing only female offspring. The mechanism of such reproductive manipulation by Wolbachia has been extensively studied. However, the effects of Wolbachia symbiosis on behavioral traits of the hosts are scarcely investigated. The parasitoid wasp Asobara japonica is an ideal insect to investigate this because symbiotic and aposymbiotic strains are available: Wolbachia-infected Tokyo (TK) and noninfected Iriomote (IR) strains originally collected on the main island and southwest islands of Japan, respectively. We compared the oviposition behaviors of the two strains and found that TK strain females parasitized Drosophila melanogaster larvae more actively than the IR strain, especially during the first two days after eclosion. Removing Wolbachia from the TK strain wasps by treatment with tetracycline or rifampicin decreased their parasitism activity to the level of the IR strain. Morphological and behavioral analyses of both strain wasps showed that Wolbachia endosymbionts do not affect development of the host female reproductive tract and eggs, but do enhance host-searching ability of female wasps. These results suggest the possibility that Wolbachia endosymbionts may promote their diffusion and persistence in the host A. japonica population not only at least partly by parthenogenesis but also by enhancement of oviposition frequency of the host females.     

Two Different Rickettsial Bacteria Invading Volvox carteri

BackgroundBacteria of the family Rickettsiaceae are principally associated with arthropods. Recently, endosymbionts of the Rickettsiaceae have been found in non-phagotrophic cells of the volvocalean green algae Carteria cerasiformis, Pleodorina japonica, and Volvox carteri. Such endosymbionts were present in only C. cerasiformis strain NIES-425 and V. carteri strain UTEX 2180, of various strains of Carteria and V. carteri examined, suggesting that rickettsial endosymbionts may have been transmitted to only a few algal strains very recently. However, in preliminary work, we detected a sequence similar to that of a rickettsial gene in the nuclear genome of V. carteri strain EVE.Conclusion/SignificanceAt least two different rickettsial organisms may have invaded the V. carteri lineage, one of which may be the direct ancestor of the endosymbiont of V. carteri strain UTEX 2180, whereas the other may be closely related to the endosymbiont of P. japonica. Endosymbiotic gene transfer from the latter rickettsial organism may have occurred in an ancestor of V. carteri. Thus, the rickettsiae may be widely associated with V. carteri, and likely have often been lost during host evolution.     

High Potential of a Transposon mPing as a Marker System in japonica �� japonica Cross in Rice

Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies. In contrast, most other japonicas, including Nipponbare, have 50 or fewer mPing insertions in their genome. In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas, Nipponbare × Gimbozu (EG4). These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism (150 of 183) than all other molecular markers tested including short sequence repeat markers (46 of 661). In addition, we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare × Gimbozu EG4, and successfully mapped a locus involved in heading date on the short arm of chromosome 6. Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10.Key words: Linkage mapping, Transposon, japonica, Oryza sativa L., QTL analysis     

Sydowia japonica, a new name for Leptosphaerulina japonica based on morphological and molecular data

We examined the taxonomic position of Leptosphaerulina japonica, a parasitic fungus on male strobili of Japanese cedar (Cryptomeria japonica) using morphology and molecular phylogeny. Because neither specimens nor illustrations were designated in the original paper, this name is neotypified with a fresh specimen collected from the type locality, Yamagata, Japan. Leptosphaerulina japonica has asci produced in a broad layer arising from the entire base of the locule, stipitate acervuli, and a hormonema-like synanamorph. These characteristics are not typical of the genus Leptosphaerulina (Didymellaceae, Pleosporales). In a molecular phylogenetic analysis of ITS sequences, L. japonica was placed into the Dothideaceae/Dothioraceae, Dothideales. Although muriform ascospores and an anamorph with long stipitate acervuli have not been reported for species in Sydowia, the other morphology and phylogeny support placement of L. japonica in that genus. Thus, a new combination, Sydowia japonica, is proposed.     

Infectivity and Arthritis Induction of Borrelia japonica on SCID Mice and Immune Competent Mice: Possible Role of Galactosylceramide Binding Activity on Initiation of Infection

We investigated the relationship between the binding activity to galactosylceramide (GalCer) and the arthritis induction activity of Borrelia japonica. The B. japonica strains maintained the ability to induce arthritis in inbred C3H/HeN and immunodeficient SCID mice, but the ability was lower than that of Borrelia burgdorferi sensu stricto virulent strain 297. Histopathological changes were restricted to the joints, and a marked effusion of polymorphonuclear neutrophils into the joint space was found. The binding activity of B. japonica strains to GalCer was lower than that of the virulent strain 297 but higher than that of the high-passage strain 297. The lower infectivity and virulence of B. japonica may explain its lower binding ability to GalCer.     

Prevalence of Onchocerca japonica and O. takaokai infections in the Japanese wild boar,Sus scrofa leucomystax,and the Ryukyu wild boar,S. s. riukiuanus,in Japan

Reports of zoonotic infections with Onchocerca japonica (Nematoda: Filarioidea), which parasitizes the Japanese wild boar, Sus scrofa leucomystax, have recently increased in Japan. To predict the occurrence of infection in humans, it is necessary to determine the prevalence of O. japonica infection in the natural host animals. We investigated the presence of adult worms in the footpads, and of microfilariae in skin snips, taken from the host animals, between 2000 and 2018. Onchocerca japonica was found in 165 of 223 (74%) Japanese wild boars in Honshu and Kyushu. Among the nine regions studied, the highest prevalence of O. japonica infection was found in Oita, Kyushu, where 47 of 52 (90.4%) animals were infected. The ears were the predilection sites for O. japonica microfilariae. Adult worms of O. japonica were found more frequently in the hindlimbs than in the forelimbs of the host animals. Onchocerca takaokai was found in 14 of 52 (26.9%) Japanese wild boars in Oita. In Kakeroma Island among the Nansei Islands, both O. japonica and O. takaokai were isolated from the Ryukyu wild boar, S. s. riukiuanus. These observations could help predict future occurrences of human zoonotic onchocercosis in Japan.     

Terminal N-Acetylgalactosamine-Specific Leguminous Lectin from Wisteria japonica as a Probe for Human Lung Squamous Cell Carcinoma

Millettia japonica was recently reclassified into the genus Wisteria japonica based on chloroplast and nuclear DNA sequences. Because the seed of Wisteria floribunda expresses leguminous lectins with unique N-acetylgalactosamine-binding specificity, we purified lectin from Wisteria japonica seeds using ion exchange and gel filtration chromatography. Glycan microarray analysis demonstrated that unlike Wisteria floribunda and Wisteria brachybotrys lectins, which bind to both terminal N-acetylgalactosamine and galactose residues, Wisteria japonica lectin (WJA) specifically bound to both α- and β-linked terminal N-acetylgalactosamine, but not galactose residues on oligosaccharides and glycoproteins. Further, frontal affinity chromatography using more than 100 2-aminopyridine-labeled and p-nitrophenyl-derivatized oligosaccharides demonstrated that the ligands with the highest affinity for Wisteria japonica lectin were GalNAcβ1-3GlcNAc and GalNAcβ1-4GlcNAc, with K _a values of 9.5 × 10⁴ and 1.4 × 10⁵ M^-1, respectively. In addition, when binding was assessed in a variety of cell lines, Wisteria japonica lectin bound specifically to EBC-1 and HEK293 cells while other Wisteria lectins bound equally to all of the cell lines tested. Wisteria japonica lectin binding to EBC-1 and HEK293 cells was dramatically decreased in the presence of N-acetylgalactosamine, but not galactose, mannose, or N-acetylglucosamine, and was completely abrogated by β-hexosaminidase-digestion of these cells. These results clearly demonstrate that Wisteria japonica lectin binds to terminal N-acetylgalactosamine but not galactose. In addition, histochemical analysis of human squamous cell carcinoma tissue sections demonstrated that Wisteria japonica lectin specifically bound to differentiated cancer tissues but not normal tissue. This novel binding characteristic of Wisteria japonica lectin has the potential to become a powerful tool for clinical applications.     

<Emphasis Type="Italic">Rf5</Emphasis> is able to partially restore fertility to Honglian-type cytoplasmic male sterile <Emphasis Type="Italic">japonica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>) lines

Three-line japonica hybrids have been developed mainly on Chinsurah Boro II (BT)-type cytoplasmic male sterile (CMS) lines of Oryza sativa L., but the unstable sterility of some BT-type CMS lines, and the threat of genetic vulnerability when using a single cytoplasm source, have inhibited their use in rice cultivation. Previously, the sterility of Honglian (HL)-type japonica CMS lines derived from common red-awned wild rice (Oryza rufipogon) has been proven to be more stable than that of BT-type japonica CMS lines. Here, we genetically characterized HL-type japonica CMS lines and the restorer-of-fertility (Rf) gene for breeding HL-type japonica hybrids. HL-type japonica CMS lines displayed stained abortive pollen grains, unlike HL-type indica CMS lines. The BT-type japonica restorer lines, which contain Rf, had different capabilities to restore HL-LiuqianxinA (HL-LqxA), an HL-type japonica CMS line, and the restorers for the HL-type japonica CMS lines could be selected from the preexisting BT-type japonica restorers in rice production. A genetic analysis showed that the restoration of normal fertility to HL-LqxA was controlled by a major gene and was affected by minor effector genes and/or modifiers. The major Rf in SiR2982, a BT-type japonica restorer, was mapped to a ~100-kb physical region on chromosome 10, and was demonstrated to be Rf5 (Rf1a) by sequencing. Furthermore, Rf5 partially restored fertility and had a dosage effect on HL-type japonica CMS lines. These results will be helpful for the development of HL-type japonica hybrids.     

Relationship between burrowing activity of the polychaetous annelid, Neanthes japonica (Izuka) and nitrification-denitrification processes in the sediments

The influence of the benthic organism, Neanthes japonica (Izuka) on nitrification-denitrification processes has been studied in experimental aquaria. The aquaria were filled with diluted sea water with or without nitrate, and contained or did not contain N. japonica. In the series supplied with diluted sea water without nitrate, extremely high concentrations of nitrite + nitrate nitrogen were found in the inner layer of the burrow wall, and denitrification activity in the surface layer (0–0.5 cm) containing N. japonica was three times that of control. In the series supplied with nitrate, there was no significant difference in the activity between surface layers with and without N. japonica. The influence of bioturbation of sediments by N. japonica on nitrification-denitrification processes and its mechanisms have been discussed.     

Homogeneity of Borrelia japonica and heterogeneity of Borrelia afzelii and 'Borrelia tanukii' isolated in Japan, determined from ospC gene sequences

Borrelia afzelii, B. japonica, and `B. tanukii' isolated from various sources and geographical origins in Japan were characterized by restriction fragment length polymorphism (RFLP) analysis and sequencing analysis of the outer surface protein C (OspC) amplicon. B. afzelii and `B. tanukii' generated variable RFLP patterns and differences in ospC gene sequence were confirmed. In contrast, 26 isolates of B. japonica generated one OspC RFLP type, and sequence similarity between B. japonica ranged from 96.4 to 99.7%. These finding suggests that B. japonica is unique in comparison with other members of B. burgdorferi sensu lato species with respect to homogeneity of the ospC gene.     

Chromosome-level genome assembly and characterization of Sophora Japonica

Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max ∼107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume whole-genome duplication events in S. japonica. We further found that multiple TF families (e.g. BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbours more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.     

Congener comparison of native (Zostera marina) and introduced (Z. japonica) eelgrass at multiple scales within a Pacific Northwest estuary

A congener comparison of native (Zostera marina) and introduced (Zostera japonica) eelgrasses was conducted in Willapa Bay, Washington, USA. Along intertidal transects, Z. japonica (0.1–1.5 m above mean lower low water [MLLW]) occurred above Z. marina (<0.6 m MLLW). Both species declined in shoot length at higher elevation, but Z. japonica was always shorter (20 vs. 100 cm) and occurred at higher shoot density (>3,800 vs. <360 m^?2 in Z. marina). Z. japonica exhibited greater seasonal variation in biomass, with increases supported by both sustained asexual reproduction (rhizome branching) and recruitment from seeds (30 vs. <5% in Z. marina). Z. japonica’s successful invasion appears related to small size and high reproductive output, allowing it to spread quickly in a variable and stressful intertidal environment where competitive effects are low. Based on interannual changes in abundance, the native eelgrass has also recently increased in Willapa Bay, and one hypothesis involves “engineering” of suitable habitat at higher tidal elevations by Z. japonica.     

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.     

Predicted potential distribution of Sydowia japonica in Japan

Sydowia japonica, a dothidealean fungus, is a parasite that is specific to the male strobili of Japanese cedar. The fungus is a candidate for the control of Japanese cedar pollen dispersal, which is a cause of pollinosis. To evaluate S. japonica for bioherbicidal applications, it is necessary to characterise its potential distribution and environmental niche. Here, we predicted the distribution of S. japonica in Japan using field surveys and a maximum entropy model, and identified the environmental variables that influence its distribution. We identified S. japonica from a total of 87 localities in Japan through field surveys. Based on presence data and associated environmental variables, our model predicted that S. japonica is widely distributed in Japan, but concentrated in the Hokuriku and Kinki areas along the Sea of Japan. The model also predicted that the most important environmental variables influencing fungal distribution were sunshine duration in the winter and precipitation in the summer. This new information will contribute to the development of bioherbicidal applications for S. japonica.