International Journal of Genomics The latest articles from Hindawi Publishing Corporation © 2015 , Hindawi Publishing Corporation . All rights reserved. Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars Mon, 12 Oct 2015 14:16:05 +0000 Tea (Camellia sinensis) is a popular beverage all over the world and a number of studies have focused on the genetic uniqueness of tea and its cultivars. However, molecular mechanisms underlying these phenomena are largely undefined. In this report, based on expression data available from public databases, we performed a series of analyses to identify genes probably relevant to the uniqueness of C. sinensis and two of its cultivars (LJ43 and ZH2). Evolutionary analyses showed that the evolutionary rates of genes involved in the pathways were not significantly different among C. sinensis, C. oleifera, and C. azalea. Interestingly, a number of gene families, including genes involved in the pathways synthesizing iconic secondary metabolites of tea plant, were significantly upregulated, expressed in C. sinensis (LJ43) when compared to C. azalea, and this may partially explain its higher content of flavonoid, theanine, and caffeine. Further investigation showed that nonsynonymous mutations may partially contribute to the differences between the two cultivars of C. sinensis, such as the chlorina and higher contents of amino acids in ZH2. Genes identified as candidates are probably relevant to the uniqueness of C. sinensis and its cultivars should be good candidates for subsequent functional analyses and marker-assisted breeding. Yan Wei, Wang Jing, Zhou Youxiang, Zhao Mingming, Gong Yan, Ding Hua, Peng Lijun, and Hu Dingjin Copyright © 2015 Yan Wei et al. All rights reserved. Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing Mon, 12 Oct 2015 08:43:35 +0000 Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries. Hongling Tian, Xiaoshuang Xu, Fusheng Zhang, Yaoqin Wang, Shuhong Guo, Xuemei Qin, and Guanhua Du Copyright © 2015 Hongling Tian et al. All rights reserved. PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction Sun, 11 Oct 2015 13:23:54 +0000 Determining protein-protein interaction (PPI) in biological systems is of considerable importance, and prediction of PPI has become a popular research area. Although different classifiers have been developed for PPI prediction, no single classifier seems to be able to predict PPI with high confidence. We postulated that by combining individual classifiers the accuracy of PPI prediction could be improved. We developed a method called protein-protein interaction prediction classifiers merger (PPCM), and this method combines output from two PPI prediction tools, GO2PPI and Phyloprof, using Random Forests algorithm. The performance of PPCM was tested by area under the curve (AUC) using an assembled Gold Standard database that contains both positive and negative PPI pairs. Our AUC test showed that PPCM significantly improved the PPI prediction accuracy over the corresponding individual classifiers. We found that additional classifiers incorporated into PPCM could lead to further improvement in the PPI prediction accuracy. Furthermore, cross species PPCM could achieve competitive and even better prediction accuracy compared to the single species PPCM. This study established a robust pipeline for PPI prediction by integrating multiple classifiers using Random Forests algorithm. This pipeline will be useful for predicting PPI in nonmodel species. Jianzhuang Yao, Hong Guo, and Xiaohan Yang Copyright © 2015 Jianzhuang Yao et al. All rights reserved. Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily Sun, 11 Oct 2015 10:28:29 +0000 CCCH zinc finger proteins, which are characterized by the presence of three cysteine residues and one histidine residue, play important roles in RNA processing in plants. Subfamily IX CCCH proteins were recently shown to function in stress tolerances. In this study, we analyzed CCCH IX genes in Zea mays, Oryza sativa, and Sorghum bicolor. These genes, which are almost intronless, were divided into four groups based on phylogenetic analysis. Microsynteny analysis revealed microsynteny in regions of some gene pairs, indicating that segmental duplication has played an important role in the expansion of this gene family. In addition, we calculated the dates of duplication by Ks analysis, finding that all microsynteny blocks were formed after the monocot-eudicot divergence. We found that deletions, multiplications, and inversions were shown to have occurred over the course of evolution. Moreover, the Ka/Ks ratios indicated that the genes in these three grass species are under strong purifying selection. Finally, we investigated the evolutionary patterns of some gene pairs conferring tolerance to abiotic stress, laying the foundation for future functional studies of these transcription factors. Wei-Jun Chen, Yang Zhao, Xiao-Jian Peng, Qing Dong, Jing Jin, Wei Zhou, Bei-Jiu Cheng, and Qing Ma Copyright © 2015 Wei-Jun Chen et al. All rights reserved. Spaced Seed Data Structures for De Novo Assembly Sun, 11 Oct 2015 07:49:49 +0000 De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction. Inanç Birol, Justin Chu, Hamid Mohamadi, Shaun D. Jackman, Karthika Raghavan, Benjamin P. Vandervalk, Anthony Raymond, and René L. Warren Copyright © 2015 Inanç Birol et al. All rights reserved. Environment-Living Organism’s Interactions from Physiology to Genomics Wed, 07 Oct 2015 12:27:01 +0000 Shao Hongbo, Chen Sixue, and Marian Brestic Copyright © 2015 Shao Hongbo et al. All rights reserved. A Comparison Effect of Copper Nanoparticles versus Copper Sulphate on Juvenile Epinephelus coioides: Growth Parameters, Digestive Enzymes, Body Composition, and Histology as Biomarkers Wed, 07 Oct 2015 07:01:41 +0000 Copper nanoparticles (Cu-NPs) are components in numerous commercial products, but little is known about their potential hazard in the marine environments. In this study the effects of Cu-NPs and soluble Cu on juvenile Epinephelus coioides were investigated. The fish were exposed in triplicate to control, 20 or 100 µg Cu L−1 as either copper sulphate (CuSO4) or Cu-NPs for 25 days. The growth performance decreased with increasing CuSO4 or Cu-NPs dose, more so in the CuSO4 than Cu-NPs treatment. Both forms of Cu exposure inhibited activities of digestive enzymes (protease, amylase, and lipase) found in liver, stomach, and intestine. With an increase in CuSO4 and Cu-NPs dose, crude protein and crude lipid decreased, but ash and moisture increased, more so in the CuSO4 than Cu-NPs treatment. The Cu-NPs treatment caused pathologies in liver and gills, and the kinds of pathologies were broadly of the same type as with CuSO4. With an increase in CuSO4 or Cu-NPs dose, the total polyunsaturated fatty acids decreased, but total monounsaturated fatty acids and total saturated fatty acids increased compared to control. Overall, these data showed that Cu-NPs had a similar type of toxic effects as CuSO4, but soluble Cu was more toxic than Cu-NPs. Tao Wang, Xiaohua Long, Yongzhou Cheng, Zhaopu Liu, and Shaohua Yan Copyright © 2015 Tao Wang et al. All rights reserved. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) Sun, 04 Oct 2015 11:53:42 +0000 Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage. Qian Ding, Jingjuan Li, Fengde Wang, Yihui Zhang, Huayin Li, Jiannong Zhang, and Jianwei Gao Copyright © 2015 Qian Ding et al. All rights reserved. Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China Sun, 04 Oct 2015 09:18:18 +0000 Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and (). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with , tend to affect the abundance of denitrifiers. Neng Yi, Yan Gao, Zhenhua Zhang, Yan Wang, Xinhong Liu, Li Zhang, and Shaohua Yan Copyright © 2015 Neng Yi et al. All rights reserved. The SsDREB Transcription Factor from the Succulent Halophyte Suaeda salsa Enhances Abiotic Stress Tolerance in Transgenic Tobacco Sun, 04 Oct 2015 07:33:14 +0000 Dehydration-responsive element-binding (DREB) transcription factor (TF) plays a key role for abiotic stress tolerance in plants. In this study, a novel cDNA encoding DREB transcription factor, designated SsDREB, was isolated from succulent halophyte Suaeda salsa. This protein was classified in the A-6 group of DREB subfamily based on multiple sequence alignments and phylogenetic characterization. Yeast one-hybrid assays showed that SsDREB protein specifically binds to the DRE sequence and could activate the expression of reporter genes in yeast, suggesting that the SsDREB protein was a CBF/DREB transcription factor. Real-time RT-PCR showed that SsDREB was significantly induced under salinity and drought stress. Overexpression of SsDREB cDNA in transgenic tobacco plants exhibited an improved salt and drought stress tolerance in comparison to the nontransformed controls. The transgenic plants revealed better growth, higher chlorophyll content, and net photosynthesis rate, as well as higher level of proline and soluble sugars. The semiquantitative PCR of transgenics showed higher expression of stress-responsive genes. These data suggest that the SsDREB transcription factor is involved in the regulation of salt stress tolerance in tobacco by the activation of different downstream gene expression. Xu Zhang, Xiaoxue Liu, Lei Wu, Guihong Yu, Xiue Wang, and Hongxiang Ma Copyright © 2015 Xu Zhang et al. All rights reserved. Changes in the Physiological Parameters of SbPIP1-Transformed Wheat Plants under Salt Stress Thu, 01 Oct 2015 08:35:07 +0000 The SbPIP1 gene is a new member of the plasma membrane major intrinsic gene family cloned from the euhalophyte Salicornia bigelovii Torr. In order to understand the physiological responses in plants that are mediated by the SbPIP1 gene, SbPIP1-overexpressing wheat lines and WT plants of the wheat cv. Ningmai 13 were treated with salt stress. Several physiological parameters, such as the proline content, the malondialdehyde (MDA) content, and the content of soluble sugars and proteins, were compared between SbPIP1-transformed lines and WT plants under normal growth or salt stress conditions. The results indicate that overexpression of the SbPIP1 gene can increase the accumulation of the osmolyte proline, decrease the MDA content, and enhance the soluble sugar biosynthesis in the early period but has no influence on the regulation of soluble protein biosynthesis in wheat. The results suggest that SbPIP1 contributes to salt tolerance by facilitating the accumulation of the osmolyte proline, increasing the antioxidant response, and increasing the biosynthesis of soluble sugar in the early period. These results indicate SbPIP1 plays an important role in the salt stress response. Overexpression of SbPIP1 might be used to improve the salt tolerance of important crop plants. G. H. Yu, X. Zhang, and H. X. Ma Copyright © 2015 G. H. Yu et al. All rights reserved. The Calcium Sensor CBL-CIPK Is Involved in Plant’s Response to Abiotic Stresses Thu, 01 Oct 2015 08:34:35 +0000 Abiotic stress halts the physiological and developmental process of plant. During stress condition, CBL-CIPK complex is identified as a primary element of calcium sensor to perceive environmental signals. Recent studies established that this complex regulates downstream targets like ion channels and transporters in adverse stages conditions. Crosstalks between the CBL-CIPK complex and different abiotic stresses can extend our research area, which can improve and increase the production of genetically modified crops in response to abiotic stresses. How this complex links with environmental signals and creates adjustable circumstances under unfavorable conditions is now one of the burning issues. Diverse studies are already underway to delineate this signalling mechanism underlying different interactions. Therefore, up to date experimental results should be concisely published, thus paving the way for further research. The present review will concisely recapitulate the recent and ongoing research progress of positive ions (Mg2+, Na+, and K+), negative ions (, ), and hormonal signalling, which are evolving from accumulating results of analyses of CBL and CIPK loss- or gain-of-function experiments in different species along with some progress and perspectives of our works. In a word, this review will give one step forward direction for more functional studies in this area. S. M. Nuruzzaman Manik, Sujuan Shi, Jingjing Mao, Lianhong Dong, Yulong Su, Qian Wang, and Haobao Liu Copyright © 2015 S. M. Nuruzzaman Manik et al. All rights reserved. Water Properties Influencing the Abundance and Diversity of Denitrifiers on Eichhornia crassipes Roots: A Comparative Study from Different Effluents around Dianchi Lake, China Thu, 01 Oct 2015 08:17:14 +0000 To evaluate effects of environmental conditions on the abundance and communities of three denitrifying genes coding for nitrite (nirK, nirS) reductase and nitrous oxide (nosZ) reductase on the roots of Eichhornia crassipes from 11 rivers flowing into the northern part of Dianchi Lake. The results showed that the abundance and community composition of denitrifying genes on E. crassipes root varied with different rivers. The nirK gene copies abundance was always greater than that of nirS gene on the roots of E. crassipes, suggesting that the surface of E. crassipes roots growth in Dianchi Lake was more suitable for the growth of nirK-type denitrifying bacteria. The DGGE results showed significant differences in diversity of denitrifying genes on the roots of E. crassipes among the 11 rivers. Using redundancy analysis (RDA), the correlations of denitrifying microbial community compositions with environmental factors revealed that water temperature (T), dissolved oxygen (DO), and pH were relatively important environmental factors to modifying the community structure of the denitrifying genes attached to the root of E. crassipes. The results indicated that the specific environmental conditions related to different source of rivers would have a stronger impact on the development of denitrifier communities on E. crassipes roots. Neng Yi, Yan Gao, Zhenhua Zhang, Hongbo Shao, and Shaohua Yan Copyright © 2015 Neng Yi et al. All rights reserved. Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs Wed, 30 Sep 2015 13:01:39 +0000 Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is , where is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is with compounds of maximal length . In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results. Chun-Yuan Lin, Chung-Hung Wang, Che-Lun Hung, and Yu-Shiang Lin Copyright © 2015 Chun-Yuan Lin et al. All rights reserved. Corrigendum to “Heat Shock Protein 70 and 90 Genes in the Harmful Dinoflagellate Cochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses” Mon, 21 Sep 2015 08:58:44 +0000 Ruoyu Guo, Seok Hyun Youn, and Jang-Seu Ki Copyright © 2015 Ruoyu Guo et al. All rights reserved. Challenges of the Unknown: Clinical Application of Microbial Metagenomics Mon, 14 Sep 2015 09:38:39 +0000 Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology. The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods. A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination. An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage. In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres. Graham Rose, David J. Wooldridge, Catherine Anscombe, Edward T. Mee, Raju V. Misra, and Saheer Gharbia Copyright © 2015 Graham Rose et al. All rights reserved. Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement Thu, 10 Sep 2015 12:44:55 +0000 The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus ( genome), B. rapa ( genome), and its hybrid F1 ( genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement. Jinfang Zhang, Guangrong Li, Haojie Li, Xiaobin Pu, Jun Jiang, Liang Chai, Benchuan Zheng, Cheng Cui, Zujun Yang, Yongqing Zhu, and Liangcai Jiang Copyright © 2015 Jinfang Zhang et al. All rights reserved. Exploring the Functional Disorder and Corresponding Key Transcription Factors in Intraductal Papillary Mucinous Neoplasms Progression Thu, 03 Sep 2015 11:11:57 +0000 This study has analyzed the gene expression patterns of an IPMN microarray dataset including normal pancreatic ductal tissue (NT), intraductal papillary mucinous adenoma (IPMA), intraductal papillary mucinous carcinoma (IPMC), and invasive ductal carcinoma (IDC) samples. And eight clusters of differentially expressed genes (DEGs) with similar expression pattern were detected by -means clustering. Then a survey map of functional disorder in IPMN progression was established by functional enrichment analysis of these clusters. In addition, transcription factors (TFs) enrichment analysis was used to detect the key TFs in each cluster of DEGs, and three TFs (FLI1, ERG, and ESR1) were found to significantly regulate DEGs in cluster 1, and expression of these three TFs was validated by qRT-PCR. All these results indicated that these three TFs might play key roles in the early stages of IPMN progression. Guiying Bai, Chenxuan Wu, Yingtang Gao, and Guiming Shu Copyright © 2015 Guiying Bai et al. All rights reserved. An Omics Perspective on Molecular Biomarkers for Diagnosis, Prognosis, and Therapeutics of Cholangiocarcinoma Wed, 02 Sep 2015 13:05:22 +0000 Cholangiocarcinoma (CCA) is an aggressive biliary tract malignancy arising from the epithelial bile duct. The lack of early diagnostic biomarkers as well as therapeutic measures results in severe outcomes and poor prognosis. Thus, effective early diagnostic, prognostic, and therapeutic biomarkers are required to improve the prognosis and prolong survival rates in CCA patients. Recent advancement in omics technologies combined with the integrative experimental and clinical validations has provided an insight into the underlying mechanism of CCA initiation and progression as well as clues towards novel biomarkers. This work highlights the discovery and validation of molecular markers in CCA identified through omics approaches. The possible roles of these molecules in various cellular pathways, which render CCA carcinogenesis and progression, will also be discussed. This paper can serve as a reference point for further investigations to yield deeper understanding in the complex feature of this disease, potentially leading to better approaches for diagnosis, prognosis, and therapeutics. Pattaya Seeree, Phorutai Pearngam, Supeecha Kumkate, and Tavan Janvilisri Copyright © 2015 Pattaya Seeree et al. All rights reserved. Genomic Copy Number Variation Affecting Genes Involved in the Cell Cycle Pathway: Implications for Somatic Mosaicism Tue, 01 Sep 2015 13:52:46 +0000 Somatic genome variations (mosaicism) seem to represent a common mechanism for human intercellular/interindividual diversity in health and disease. However, origins and mechanisms of somatic mosaicism remain a matter of conjecture. Recently, it has been hypothesized that zygotic genomic variation naturally occurring in humans is likely to predispose to nonheritable genetic changes (aneuploidy) acquired during the lifetime through affecting cell cycle regulation, genome stability maintenance, and related pathways. Here, we have evaluated genomic copy number variation (CNV) in genes implicated in the cell cycle pathway (according to Kyoto Encyclopedia of Genes and Genomes/KEGG) within a cohort of patients with intellectual disability, autism, and/or epilepsy, in which the phenotype was not associated with genomic rearrangements altering this pathway. Benign CNVs affecting 20 genes of the cell cycle pathway were detected in 161 out of 255 patients (71.6%). Among them, 62 individuals exhibited >2 CNVs affecting the cell cycle pathway. Taking into account the number of individuals demonstrating CNV of these genes, a support for this hypothesis appears to be presented. Accordingly, we speculate that further studies of CNV burden across the genes implicated in related pathways might clarify whether zygotic genomic variation generates somatic mosaicism in health and disease. Ivan Y. Iourov, Svetlana G. Vorsanova, Maria A. Zelenova, Sergei A. Korostelev, and Yuri B. Yurov Copyright © 2015 Ivan Y. Iourov et al. All rights reserved. Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data Mon, 31 Aug 2015 12:11:12 +0000 The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity of transcription factors to their specific DNA binding sites, affecting the transcription rates of genes. In our previous research, we found that genes controlling the sensory perception of smell and genes involved in antigen processing and presentation were overrepresented significantly among genes with high SNP contents in their promoter regions. The goal of our study was to reveal functional features of human genes containing extremely small numbers of SNPs in promoter regions. Two functional groups were found to be overrepresented among genes whose promoters did not contain SNPs: (1) genes involved in gene-specific transcription and (2) genes controlling chromatin organization. We revealed that the 5′-regulatory regions of genes encoding transcription factors and chromatin-modifying proteins were characterized by reduced genetic variability. One important exception from this rule refers to genes encoding transcription factors with zinc-coordinating DNA-binding domains (DBDs), which underwent extensive expansion in vertebrates, particularly, in primate evolution. Hence, we obtained new evidence for evolutionary forces shaping variability in 5′-regulatory regions of genes. Elena V. Ignatieva, Victor G. Levitsky, and Nikolay A. Kolchanov Copyright © 2015 Elena V. Ignatieva et al. All rights reserved. The Major Prognostic Features of Nuclear Receptor NR5A2 in Infiltrating Ductal Breast Carcinomas Sun, 23 Aug 2015 12:41:36 +0000 Background. Gene expression profiles of 181 breast cancer samples were analyzed to identify prognostic features of nuclear receptors NR5A1 and NR5A2 based upon their associated transcriptional networks. Methods. A supervised network analysis approach was used to build the NR5A-mediated transcriptional regulatory network. Other bioinformatic tools and statistical methods were utilized to confirm and extend results from the network analysis methodology. Results. NR5A2 expression is a negative factor in breast cancer prognosis in both ER(−) and ER(−)/ER(+) mixed cohorts. The clinical and cohort significance of NR5A2-mediated transcriptional activities indicates that it may have a significant role in attenuating grade development and cancer related signal transduction pathways. NR5A2 signature that conditions poor prognosis was identified based upon results from 15 distinct probes. Alternatively, the expression of NR5A1 predicts favorable prognosis when concurrent NR5A2 expression is low. A favorable signature of eight transcription factors mediated by NR5A1 was also identified. Conclusions. Correlation of poor prognosis and NR5A2 activity is identified by NR5A2-mediated 15-gene signature. NR5A2 may be a potential drug target for treating a subset of breast cancer tumors across breast cancer subtypes, especially ER(−) breast tumors. The favorable prognostic feature of NR5A1 is predicted by NR5A1-mediated 8-gene signature. Li-Yun Chang, Li-Yu D. Liu, Don A. Roth, Wen-Hung Kuo, Hsiao-Lin Hwa, King-Jen Chang, and Fon-Jou Hsieh Copyright © 2015 Li-Yun Chang et al. All rights reserved. Isolation, Expression, and Promoter Analysis of GbWRKY2: A Novel Transcription Factor Gene from Ginkgo biloba Sun, 16 Aug 2015 07:37:09 +0000 WRKY transcription factor is involved in multiple life activities including plant growth and development as well as biotic and abiotic responses. We identified 28 WRKY genes from transcriptome data of Ginkgo biloba according to conserved WRKY domains and zinc finger structure and selected three WRKY genes, which are GbWRKY2, GbWRKY16, and GbWRKY21, for expression pattern analysis. GbWRKY2 was preferentially expressed in flowers and strongly induced by methyl jasmonate. Here, we cloned the full-length cDNA and genomic DNA of GbWRKY2. The full-length cDNA of GbWRKY2 was 1,713 bp containing a 1,014 bp open reading frame encoding a polypeptide of 337 amino acids. The GbWRKY2 genomic DNA had one intron and two exons. The deduced GbWRKY2 contained one WRKY domain and one zinc finger motif. GbWRKY2 was classified into Group II WRKYs. Southern blot analysis revealed that GbWRKY2 was a single copy gene in G. biloba. Many cis-acting elements related to hormone and stress responses were identified in the 1,363 bp-length 5′-flanking sequence of GbWRKY2, including W-box, ABRE-motif, MYBCOREs, and PYRIMIDINE-boxes, revealing the molecular mechanism of upregulated expression of GbWRKY2 by hormone and stress treatments. Further functional characterizations in transiently transformed tobacco leaves allowed us to identify the region that can be considered as the minimal promoter. Yong-Ling Liao, Yong-Bao Shen, Jie Chang, Wei-Wei Zhang, Shui-Yuan Cheng, and Feng Xu Copyright © 2015 Yong-Ling Liao et al. All rights reserved. Genetics of Human and Canine Dilated Cardiomyopathy Wed, 22 Jul 2015 13:55:04 +0000 Cardiovascular disease is a leading cause of death in both humans and dogs. Dilated cardiomyopathy (DCM) accounts for a large number of these cases, reported to be the third most common form of cardiac disease in humans and the second most common in dogs. In human studies of DCM there are more than 50 genetic loci associated with the disease. Despite canine DCM having similar disease progression to human DCM studies into the genetic basis of canine DCM lag far behind those of human DCM. In this review the aetiology, epidemiology, and clinical characteristics of canine DCM are examined, along with highlighting possible different subtypes of canine DCM and their potential relevance to human DCM. Finally the current position of genetic research into canine and human DCM, including the genetic loci, is identified and the reasons many studies may have failed to find a genetic association with canine DCM are reviewed. Siobhan Simpson, Jennifer Edwards, Thomas F. N. Ferguson-Mignan, Malcolm Cobb, Nigel P. Mongan, and Catrin S. Rutland Copyright © 2015 Siobhan Simpson et al. All rights reserved. Genetic Geostatistical Framework for Spatial Analysis of Fine-Scale Genetic Heterogeneity in Modern Populations: Results from the KORA Study Thu, 16 Jul 2015 10:37:40 +0000 Aiming to investigate fine-scale patterns of genetic heterogeneity in modern humans from a geographic perspective, a genetic geostatistical approach framed within a geographic information system is presented. A sample collected for prospective studies in a small area of southern Germany was analyzed. None indication of genetic heterogeneity was detected in previous analysis. Socio-demographic and genotypic data of German citizens were analyzed (212 SNPs; ). Genetic heterogeneity was evaluated with observed heterozygosity (). Best-fitting spatial autoregressive models were identified, using socio-demographic variables as covariates. Spatial analysis included surface interpolation and geostatistics of observed and predicted patterns. Prediction accuracy was quantified. Spatial autocorrelation was detected for both socio-demographic and genetic variables. Augsburg City and eastern suburban areas showed higher values. The selected model gave best predictions in suburban areas. Fine-scale patterns of genetic heterogeneity were observed. In accordance to literature, more urbanized areas showed higher levels of admixture. This approach showed efficacy for detecting and analyzing subtle patterns of genetic heterogeneity within small areas. It is scalable in number of loci, even up to whole-genome analysis. It may be suggested that this approach may be applicable to investigate the underlying genetic history that is, at least partially, embedded in geographic data. A. N. Diaz-Lacava, M. Walier, D. Holler, M. Steffens, C. Gieger, C. Furlanello, C. Lamina, H. E. Wichmann, and T. Becker Copyright © 2015 A. N. Diaz-Lacava et al. All rights reserved. Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica Sun, 12 Jul 2015 08:25:10 +0000 Transcriptome analysis was conducted in two popular Lagerstroemia cultivars: “Natchez” (NAT), a white flower and powdery mildew resistant interspecific hybrid and “Carolina Beauty” (CAB), a red flower and powdery mildew susceptible L. indica cultivar. RNA-seq reads were generated from Erysiphe australiana infected leaves and de novo assembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85% of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesis pathway (antioxidant activities or flower coloration). Furthermore, 5 of the 12 assembled unigenes in benzoxazinoid biosynthesis and 7 of 11 in flavonoid biosynthesis showed higher transcript abundance in NAT. The relative abundance of transcripts for 16 candidate DEGs (9 from CAB and 7 from NAT) detected by qRT-PCR showed general agreement with the abundances of the assembled transcripts in NAT. This study provided the first transcriptome analyses in L. indica. The differential transcript abundance between two genotypes indicates that it is possible to identify candidate genes that are associated with the plant defenses or flower coloration. Xinwang Wang, Weibing Shi, and Timothy Rinehart Copyright © 2015 Xinwang Wang et al. All rights reserved. Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species Sun, 05 Jul 2015 08:28:52 +0000 Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB), whereas B. animalis is a non-HRB species, several of the differences in these species’ gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics. Toshitaka Odamaki, Ayako Horigome, Hirosuke Sugahara, Nanami Hashikura, Junichi Minami, Jin-zhong Xiao, and Fumiaki Abe Copyright © 2015 Toshitaka Odamaki et al. All rights reserved. The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars Tue, 23 Jun 2015 09:52:02 +0000 We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide. Michihiko Shimomura, Hiroyuki Kanamori, Setsuko Komatsu, Nobukazu Namiki, Yoshiyuki Mukai, Kanako Kurita, Kaori Kamatsuki, Hiroshi Ikawa, Ryoichi Yano, Masao Ishimoto, Akito Kaga, and Yuichi Katayose Copyright © 2015 Michihiko Shimomura et al. All rights reserved. Proteome Analysis for Understanding Abiotic Stress (Salinity and Drought) Tolerance in Date Palm (Phoenix dactylifera L.) Thu, 18 Jun 2015 09:37:27 +0000 This study was carried out to study the proteome of date palm under salinity and drought stress conditions to possibly identify proteins involved in stress tolerance. For this purpose, three-month-old seedlings of date palm cultivar “Sagie” were subjected to drought (27.5 g/L polyethylene glycol 6000) and salinity stress conditions (16 g/L NaCl) for one month. DIGE analysis of protein extracts identified 47 differentially expressed proteins in leaves of salt- and drought-treated palm seedlings. Mass spectrometric analysis identified 12 proteins; three out of them were significantly changed under both salt and drought stress, while the other nine were significantly changed only in salt-stressed plants. The levels of ATP synthase alpha and beta subunits, an unknown protein and some of RubisCO fragments were significantly changed under both salt and drought stress conditions. Changes in abundance of superoxide dismutase, chlorophyll A-B binding protein, light-harvesting complex1 protein Lhca1, RubisCO activase, phosphoglycerate kinase, chloroplast light-harvesting chlorophyll a/b-binding protein, phosphoribulokinase, transketolase, RubisCO, and some of RubisCO fragments were significant only for salt stress. Haddad A. El Rabey, Abdulrahman L. Al-Malki, Khalid O. Abulnaja, and Wolfgang Rohde Copyright © 2015 Haddad A. El Rabey et al. All rights reserved. Polymorphisms of Leptin (-2548 G/A) and Leptin Receptor (Q223R) Genes in Iranian Women with Breast Cancer Sun, 14 Jun 2015 11:19:41 +0000 Recent studies have shown that polymorphisms in leptin and leptin receptor genes are associated with increased risk for breast cancer. This study aimed at investigating -2548 G/A polymorphism in leptin gene and Q223R polymorphism in leptin receptor gene in patients with breast cancer. The study included 45 women with breast cancer and 41 healthy women. PCR-RFLP was used to determine the genotype of the subjects in terms of -2548 G/A polymorphism in leptin gene and Q223R polymorphism in leptin receptor gene. Serum levels of leptin were also measured by ELISA. For -2548 G/A polymorphism, the genotypes were homozygous AA (OR = 1.13; ) and heterozygous GA (OR = 0.41; ) and for Q223R polymorphism, the genotypes were homozygous RR (OR = 6.7; ) and heterozygous QR (OR = 8.3; ). The mean serum level of leptin was 33.22 ± 21.35 ng/mL in patients and 29.49 ± 23.27 ng/mL in the normal participants (). Although, despite the magnitude of the associations, the results suggested no statistically significant contribution of -2548 G/A polymorphism (in leptin gene), Q223R polymorphism (in leptin receptor gene), and serum leptin levels in predicting the risk of breast cancer, further studies with larger sample size are suggested. Reza Mahmoudi, Bahareh Noori Alavicheh, Mohammad Amin Nazer Mozaffari, Mohammad Fararouei, and Mohsen Nikseresht Copyright © 2015 Reza Mahmoudi et al. All rights reserved.