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Kim S.,Seoul National University | Kim M.-S.,Seoul National University | Kim Y.-M.,Korea Research Institute of Bioscience and Biotechnology | Yeom S.-I.,Seoul National University | And 9 more authors.
DNA Research | Year: 2015

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Source

Na Y.-E.,National Institute of Agricultural Science | Jung J.W.,Incheon National University | Kwon H.W.,Incheon National University
Journal of Asia-Pacific Entomology | Year: 2016

Transient Receptor Potential (TRP) channels respond to diverse stimuli and function as primary regulators of sensory information such as olfaction and auditory. TRP proteins are activated by several chemicals and secondary messengers to modulate communications between cell to cell as well as to recognize some environmental changes. Here we report on the identification and localization of the Aedes aegypti homolog of the TRPV channel proteins that is conserved to other insect species based on comparison of amino acids sequences similarities. Transcripts of two TRPV proteins homologous to Drosophila TRPV proteins (Nan and Iav) were ubiquitously expressed in the whole tissues such as antennae, maxillary palps, proboscis, legs, and body of the mosquito. Indeed, TRPV channel family members were localized in sensilla chaetica and sensilla basiconica on the antennae as well as ciliary segment of Johnston's organs. Taken together, we infer that TRPV channels of Aedes aegypti may function as both a sound sensor involved in detection of sound signals and as a chemical sensor responding attractants or repellent compounds allowing them to respond to the appearance of predators or other environmental chemical cues at a distance with behaviors crucial for survival. © 2016 . Source

Nanjo Y.,Japan National Agriculture and Food Research Organization | Maruyama K.,Japan International Research Center for Agricultural science | Yasue H.,National Institute of Agricultural Science | Yasue H.,Tsukuba GeneTechnology Laboratories Inc. | And 4 more authors.
Plant Molecular Biology | Year: 2011

To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings. © 2011 Springer Science+Business Media B.V. Source

Haque M.M.,Gyeongsang National University | Kim G.W.,Gyeongsang National University | Kim P.J.,Gyeongsang National University | Kim S.Y.,National Institute of Agricultural Science
Field Crops Research | Year: 2016

Midseason drainage is regarded as a key practice to suppress methane (CH4) emission from paddy soil during rice cultivation, but it can increase carbon dioxide (CO2) and nitrous oxide (N2O) emissions. However, the influences of midseason drainage practice on the net global warming potential (GWP) and greenhouse gas intensity (GHGI) of rice cropping systems is not well documented in the East monsoon region. In this field study, the effect of a 30-day midseason drainage practice from the 28th day after transplanting (DAT) to the 57th DAT on the three major greenhouse gas (GHG) fluxes and yield properties were compared with those of a continuous flooding system during rice cultivation in 2011 and 2012. The impact of midseason drainage on changing three GHG emissions was compared using the GWP value and GHG intensity (GHGI). Midseason drainage significantly reduced the net GWP scale by 46-50% of the continuous flooding, mainly due to 50-53% reduction of seasonal CH4 fluxes. Midseason drainage significantly increased N2O flux by 20-37% over the conventional flooding, but the influence of N2O emission increase on the net GWP scale was negligible. Midseason drainage significantly decreased soil C sequestration capacity by around 60% of continuous flooding, and then increased net GWP by 0.25-0.32Mg CO2-eq.ha-1 during rice cultivation. There was no significant difference of rice yield between two irrigation systems, and then midseason drainage can reduce GHGI by 50-56% of the continuous flooding. In conclusion, the midseason drainage practice during rice cultivation could be very useful soil management strategy to reduce GHG emission impact from lowland rice fields without impacting rice productivity. © 2016 Elsevier B.V. Source

Kim G.W.,Gyeongsang National University | Ho A.,Netherlands Institute of Ecology | Kim P.J.,Gyeongsang National University | Kim S.Y.,Gyeongsang National University | Kim S.Y.,National Institute of Agricultural Science
Waste Management | Year: 2016

The landfilling of municipal solid waste is a significant source of atmospheric methane (CH4), contributing up to 20% of total anthropogenic CH4 emissions. The evapotranspiration (ET) cover system, an alternative final cover system in waste landfills, has been considered to be a promising way to mitigate CH4 emissions, as well as to prevent water infiltration using vegetation on landfill cover soils. In our previous studies, bottom ash from coal-fired power plants was selected among several industrial residues (blast furnace slag, bottom ash, construction waste, steel manufacture slag, stone powder sludge, and waste gypsum) as the best additive for ET cover systems, with the highest mechanical performance achieved for a 35% (wtwt-1) bottom ash content in soil. In this study, to evaluate the field applicability of bottom ash mixed soil as ET cover, four sets of lysimeters (height 1.2m×width 2m×length 6m) were constructed in 2007, and four different treatments were installed: (i) soil+bottom ash (35% wtwt-1) (SB); (ii) soil+compost (2% wtwt-1, approximately corresponding to 40Mgha-1 in arable field scale) (SC); (iii) soil+bottom ash+compost (SBC); and (iv) soil only as the control (S). The effects of bottom ash mixing in ET cover soil on CH4 oxidation potential and vegetation growth were evaluated in a pilot ET cover system in the 5th year after installation by pilot experiments using the treatments. Our results showed that soil properties were significantly improved by bottom ash mixing, resulting in higher plant growth. Bottom ash addition significantly increased the CH4 oxidation potential of the ET cover soil, mainly due to improved organic matter and available copper concentration, enhancing methanotrophic abundances in soil amended with bottom ash. Conclusively, bottom ash could be a good alternative as a soil additive in the ET cover system to improve vegetation growth and mitigate CH4 emission impact in the waste landfill system. © 2016 Elsevier Ltd. Source

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