Reduced Expression of PRX2/ATPRX1, PRX8, PRX35, and PRX73 Affects Cell Elongation, Vegetative Growth, and Vasculature Structures in Arabidopsis thaliana.

Class III peroxidases (PRXs) are involved in a broad spectrum of physiological and developmental processes throughout the life cycle of plants. However, the specific function of each PRX member in the family remains largely unknown. In this study, we selected four class III peroxidase genes (PRX2/ATPRX1, PRX8, PRX35, and PRX73) from a previous genome-wide transcriptome analysis, and performed phenotypic and morphological analyses, including histochemical staining, in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi plants. The reduced mRNA levels of corresponding PRX genes in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi seedlings resulted in elongated hypocotyls and roots, and slightly faster vegetative growth. To investigate internal structural changes in the vasculature, we performed histochemical staining, which revealed alterations in cell wall structures in the main vasculature of hypocotyls, stems, and roots of each PRXRNAi plant compared to wild-type (Col-0) plants. Furthermore, we found that PRX35RNAi plants displayed the decrease in the cell wall in vascular regions, which are involved in downregulation of lignin biosynthesis and biosynthesis-regulated genes' expression. Taken together, these results indicated that the reduced expression levels of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affected hypocotyl and root elongation, vegetative growth, and the vasculature structures in hypocotyl, stem, and root tissues, suggesting that the four class III PRX genes play roles in plant developmental processes.

An Efficient Compression Method of Underwater Acoustic Sensor Signals for Underwater Surveillance.

In this paper, we propose a new compression method using underwater acoustic sensor signals for underwater surveillance. Generally, sonar applications that are used for surveillance or ocean monitoring are composed of many underwater acoustic sensors to detect significant sources of sound. It is necessary to apply compression methods to the acquired sensor signals due to data processing and storage resource limitations. In addition, depending on the purposes of the operation and the characteristics of the operating environment, it may also be necessary to apply compression methods of low complexity. Accordingly, in this research, a low-complexity and nearly lossless compression method for underwater acoustic sensor signals is proposed. In the design of the proposed method, we adopt the concepts of quadrature mirror filter (QMF)-based sub-band splitting and linear predictive coding, and we attempt to analyze an entropy coding technique suitable for underwater sensor signals. The experiments show that the proposed method achieves better performance in terms of compression ratio and processing time than popular or standardized lossless compression techniques. It is also shown that the compression ratio of the proposed method is almost the same as that of SHORTEN with a 10-bit maximum mode, and both methods achieve a similar peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) index on average.

Wood transcriptome analysis of Pinus densiflora identifies genes critical for secondary cell wall formation and NAC transcription factors involved in tracheid formation.

Although conifers have significant ecological and economic value, information on transcriptional regulation of wood formation in conifers is still limited. Here, to gain insight into secondary cell wall (SCW) biosynthesis and tracheid formation in conifers, we performed wood tissue-specific transcriptome analyses of Pinus densiflora (Korean red pine) using RNA sequencing. In addition, to obtain full-length transcriptome information, PacBio single molecule real-time iso-sequencing was carried out using RNAs from 28 tissues of P. densiflora. Subsequent comparative tissue-specific transcriptome analysis successfully pinpointed critical genes encoding key proteins involved in biosynthesis of the major secondary wall components (cellulose, galactoglucomannan, xylan and lignin). Furthermore, we predicted a total of 62 NAC (NAM, ATAF1/2 and CUC2) family transcription factor members and identified seven PdeNAC genes preferentially expressed in developing xylem tissues in P. densiflora. Protoplast-based transcriptional activation analysis found that four PdeNAC genes, homologous to VND, NST and SND/ANAC075, upregulated GUS activity driven by an SCW-specific cellulose synthase promoter. Consistently, transient overexpression of the four PdeNACs induced xylem vessel cell-like SCW deposition in both tobacco (Nicotiana benthamiana) and Arabidopsis leaves. Taken together, our data provide a foundation for further research to unravel transcriptional regulation of wood formation in conifers, especially SCW formation and tracheid differentiation.

Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies.

A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, HD1 was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination (R2) of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number.

Assessment of Metabolic Profiles in Florets of Carthamus Species Using Ultra-Performance Liquid Chromatography-Mass Spectrometry.

The genus Carthamus is a diverse group of plants belonging to the family Compositae. Florets of Carthamus species exhibit various colors, including white, yellow, orange, and red, which are related to their metabolite compositions. We aimed to investigate the metabolites accumulated in florets of three wild (C. lanatus, C. palaestinus, and C. turkestanicus) and one cultivated (C. tinctorius) species of safflower at three developmental stages. Metabolites were extracted from freeze-dried florets using 70% methanol; qualification and quantification were carried out using liquid chromatography quadrupole time-of-flight mass spectrometry in positive and negative ion modes followed by extraction of the peaks. Fifty-six metabolites, including phenylpropanoids, chalcones, isoflavonoids, flavanones, flavonols, flavones, and other primary metabolites, were identified for the first time in safflower wild species. The orange florets contained high abundances of safflomin A, anhydrosafflor yellow B, and baimaside, whereas white/cream and light-yellow pigmented florets had high abundances of 1,5-dicaffeoylquinic acid, luteolin 7-O-glucuronide, and apigenin 7-O-ß-D-glucuronide. The principal component analysis clearly distinguished the samples based on their pigment types, indicating that color is a dominant factor dictating the identity and amount of the metabolites. Pearson correlation data based on levels of metabolites showed that orange and yellow florets were significantly correlated to each other. White and cream pigmented species were also highly correlated. Comparison between three developmental stages of safflower wild species based on their metabolite profile showed inconsistent. The findings of this study broaden the current knowledge of safflower metabolism. The wide diversity of metabolites in safflower materials also helps in efforts to improve crop quality and agronomic traits.

Chitin Biosynthesis Inhibition of Meloidogyne incognita by RNAi-Mediated Gene Silencing Increases Resistance to Transgenic Tobacco Plants.

Meloidogyne incognita is a devastating plant parasitic nematode that causes root knot disease in a wide range of plants. In the present study, we investigated host-induced RNA interference (RNAi) gene silencing of chitin biosynthesis pathway genes (chitin synthase, glucose-6-phosphate isomerase, and trehalase) in transgenic tobacco plants. To develop an RNAi vector, ubiquitin (UBQ1) promoter was directly cloned, and to generate an RNAi construct, expression of three genes was suppressed using the GATEWAY system. Further, transgenic Nicotiana benthamiana lines expressing dsRNA for chitin synthase (CS), glucose-6-phosphate isomerase (GPI), and trehalase 1 (TH1) were generated. Quantitative PCR analysis confirmed endogenous mRNA expression of root knot nematode (RKN) and revealed that all three genes were more highly expressed in the female stage than in eggs and in the parasitic stage. In vivo, transformed roots were challenged with M. incognita. The number of eggs and root knots were significantly decreased by 60-90% in RNAi transgenic lines. As evident, root galls obtained from transgenic RNAi lines exhibited 0.01- to 0.70-fold downregulation of transcript levels of targeted genes compared with galls isolated from control plants. Furthermore, phenotypic characteristics such as female size and width were also marginally altered, while effect of egg mass per egg number in RNAi transgenic lines was reduced. These results indicate the relevance and significance of targeting chitin biosynthesis genes during the nematode lifespan. Overall, our results suggest that further developments in RNAi efficiency in commercially valued crops can be applied to employ RNAi against other plant parasitic nematodes.

A Convenient Plant-Based Detection System to Monitor Androgenic Compound in the Environment.

Environmental androgen analogues act as endocrine disruptors, which inhibit the normal function of androgen in animals. In the present work, through the expression of a chimeric gene specified for the production of the anthocyanin in response to androgen DHT (dihydrotestosterone), we generated an indicator Arabidopsis that displays a red color in leaves in the presence of androgen compounds. This construct consists of a ligand-binding domain of the human androgen receptor gene and the poplar transcription factor gene PtrMYB119, which is involved in anthocyanin biosynthesis in poplar and Arabidopsis. The transgenic Arabidopsis XVA-PtrMYB119 displayed a red color in leaves in response to 10 ppm DHT, whereas it did not react in the presence of other androgenic compounds. The transcript level of PtrMYB119 peaked at day 13 of DHT exposure on agar media and then declined to its normal level at day 15. Expressions of anthocyanin biosynthesis genes including chalcone flavanone isomerase, chalcone synthase, flavanone 3-hydroxylase, dihydroflavonol 4-reductase, UFGT (UGT78D2), and anthocyanidin synthase were similar to that of PtrMYB119. It is assumed that this transgenic plant can be used by nonscientists for the detection of androgen DHT in the environment and samples such as food solution without any experimental procedures.

Characterization of a novel antibacterial N-acyl amino acid synthase from soil metagenome.

In an effort to isolate novel natural antibiotics, we searched for antibacterial long-chain N-acyl amino acid synthase (NAS) genes from 70,000 soil metagenome clones by Bacillus subtilis-overlaying screening. In an antibacterial cosmid clone, YS92B, a single gene nasYPL was responsible for the production of the Nas. nasYPL was 903 bp long, and the deduced amino acid sequence showed the highest 71% identity with a hypothetical protein from Massilia niastensis. Phylogenetic analysis demonstrated that NasYPL belongs to Group 1 Nas. Heterologous expression of the same nasYPL gene in Escherichia coli and two Pseudomonas strains (P. putida and P. koreensis) conferred antibacterial activities against Listeria monocytogenes, Staphylococcus epidermidis, and Bacillus subtilis. Mass spectral analysis of the antibacterial fractions identified 7 peaks corresponding to long-chain N-acyl tyrosine, 5 peaks to N-acyl phenylalanine, and 3 peaks to N-acyl leucine (or isoleucine) derivatives linked with 7 fatty acids, indicating enzymatic products derived by NasYPL. Therefore, NasYPL expression by host-specific manner may provide applicable antibacterial characteristics to biotechnologically important Pseudomonas strains.

Defining the genome structure of 'Tongil' rice, an important cultivar in the Korean "Green Revolution".

BACKGROUND: Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the 'Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. RESULTS: A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. CONCLUSIONS: Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.

Large-scale analysis of the GRAS gene family in Arabidopsis thaliana.

GRAS proteins belong to a plant-specific transcription factor family. Currently, 33 GRAS members including a putative expressed pseudogene have been identified in the Arabidopsis genome. With a reverse genetic approach, we have constructed a "phenome-ready unimutant collection" of the GRAS genes in Arabidopsis thaliana. Of this collection, we focused on loss-of-function mutations in 23 novel GRAS members. Under standard conditions, homozygous mutants have no obvious morphological phenotypes compared with those of wild-type plants. Expression analysis of GRAS genes using quantitative real-time RT-PCR (qRT-PCR), microarray data mining, and promoter::GUS reporter fusions revealed their tissue-specific expression patterns. Our analysis of protein-protein interaction and subcellular localization of individual GRAS members indicated their roles as transcription regulators. In our yeast two-hybrid (Y2H) assay, we confirmed the protein-protein interaction between SHORT-ROOT (SHR) and SCARECROW (SCR). Furthermore, we identified a new SHR-interacting protein, SCARECROW-LIKE23 (SCL23), which is the most closely related to SCR. Our large-scale analysis provides a comprehensive evaluation on the Arabidopsis GRAS members, and also our phenome-ready unimutant collection will be a useful resource to better understand individual GRAS proteins that play diverse roles in plant growth and development.

The tobacco gene Ntcyc07 confers arsenite tolerance in Saccharomyces cerevisiae by reducing the steady state levels of intracellular arsenic.

We cloned a plant gene, Ntcyc07, conferring arsenite tolerance by expressing a tobacco expression library in WT yeast (Y800). Expression of Ntcyc07 increased the tolerance to As(III) and decreased its accumulation, suggesting that the enhanced As(III) tolerance resulted from a reduction of the intracellular arsenic level. Interestingly, expression of Ntcyc07 increased the expression of the As(III) export carrier ACR3, but repressed that of As(III) uptake channel FPS1. Ntcyc07p interacted with Acr1p, which is the transcriptional activator of ACR3, but not with the ACR3 promoter. Taken together, the data indicated that Ntcyc07p promoted As(III) tolerance by decreasing the intracellular level of As(III) via increasing the expression of ACR3 and reducing that of FPS1.

Wound-induced expression of the ferulate 5-hydroxylase gene in Camptotheca acuminata.

The phenylpropanoid pathway plays important roles in plants following exposure to environmental stresses, such as wounding and pathogen attack, which lead to the production of a variety of compounds, including lignin, flavonoids and phytoalexins. Ferulate 5-hydroxylase (F5H) is a cytochrome P450-dependent monooxygenase that catalyses the hydroxylation of ferulic acid, coniferaldehyde and coniferyl alcohol, leading to sinapic acid and syringyl lignin biosynthesis. We isolated F5H cDNA and genomic DNA from Camptotheca acuminata and investigated the expression pattern of the C. acuminata F5H (CaF5H1) gene in response to wounding. A search against the BLOCKS database of conserved protein motifs indicated that CaF5H1 retains features in common with F5Hs reported from other plants. 5'-flanking region analysis using the PLACE database showed that putative regulatory elements related to various abiotic and biotic stresses, such as drought, wounding, low temperature and pathogens, exist in the 5'-flanking region of CaF5H1. Based upon these analysis results, we investigated the expression pattern of CaF5H1 gene in response to wounding and stress-related molecules. Here, we show that CaF5H1 transcripts accumulated in the leaves in response to mechanical wounding or the application of molecules involved in the stress response, such as ethylene, ABA and hydrogen peroxide (H2O2). The application of salicylic acid and diphenylene iodonium (DPI) inhibited the wound-induced expression of CaF5H1. Taken together, we suggest that wound-induced expression of CaF5H1 may be mediated by MJ and H2O2 and enhanced phenylpropanoid contents via CaF5H1 maybe function in response to various stresses, including wounding, in plants.