International Journal of Genomics The latest articles from Hindawi Publishing Corporation © 2016 , Hindawi Publishing Corporation . All rights reserved. Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers Sun, 10 Jan 2016 12:07:16 +0000 Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp. Bharat Bhusan Patnaik, So Young Park, Se Won Kang, Hee-Ju Hwang, Tae Hun Wang, Eun Bi Park, Jong Min Chung, Dae Kwon Song, Changmu Kim, Soonok Kim, Jae Bong Lee, Heon Cheon Jeong, Hong Seog Park, Yeon Soo Han, and Yong Seok Lee Copyright © 2016 Bharat Bhusan Patnaik et al. All rights reserved. Plant Comparative and Functional Genomics Thu, 31 Dec 2015 09:07:35 +0000 Xiaohan Yang, Jim Leebens-Mack, Feng Chen, and Yanbin Yin Copyright © 2015 Xiaohan Yang et al. All rights reserved. Quantification and Gene Expression Analysis of Histone Deacetylases in Common Bean during Rust Fungal Inoculation Mon, 28 Dec 2015 09:33:22 +0000 Histone deacetylases (HDACs) play an important role in plant growth, development, and defense processes and are one of the primary causes of epigenetic modifications in a genome. There was only one study reported on epigenetic modifications of the important legume crop, common bean, and its interaction with the fungal rust pathogen Uromyces appendiculatus prior to this project. We measured the total active HDACs levels in leaf tissues and observed expression patterns for the selected HDAC genes at 0, 12, and 84 hours after inoculation in mock inoculated and inoculated plants. Colorimetric analysis showed that the total amount of HDACs present in the leaf tissue decreased at 12 hours in inoculated plants compared to mock inoculated control plants. Gene expression analyses indicated that the expression pattern of gene PvSRT1 is similar to the trend of total active HDACs in this time course experiment. Gene PvHDA6 showed increased expression in the inoculated plants during the time points measured. This is one of the first attempts to study expression levels of HDACs in economically important legumes in the context of plant pathogen interactions. Findings from our study will be helpful to understand trends of total active HDACs and expression patterns of these genes under study during biotic stress. Kalpalatha Melmaiee, Venu (Kal) Kalavacharla, Adrianne Brown, Antonette Todd, Yaqoob Thurston, and Sathya Elavarthi Copyright © 2015 Kalpalatha Melmaiee et al. All rights reserved. Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population Sun, 27 Dec 2015 13:10:07 +0000 Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip. Tae-Joon Park, Lyong Heo, Sanghoon Moon, Young Jin Kim, Ji Hee Oh, Sohee Han, and Bong-Jo Kim Copyright © 2015 Tae-Joon Park et al. All rights reserved. Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species Sun, 13 Dec 2015 09:21:36 +0000 Leucine-rich repeat receptor-like kinases (LRR-RLKs) make up the largest group of RLKs in plants and play important roles in many key biological processes such as pathogen response and signal transduction. To date, most studies on LRR-RLKs have been conducted on model plants. Here, we identified 236 and 230 LRR-RLKs in two industrial oil-producing trees: Vernicia fordii and Vernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among the Vf/VmLRR-RLKs. The conserved motif of the LRR domain in Vf/VmLRR-RLKs matched well the known plant LRR consensus sequence but differed at the third last amino acid (W or L). Phylogenetic analysis revealed that Vf/VmLRR-RLKs were grouped into 16 subclades. We characterized the expression profiles of Vf/VmLRR-RLKs in various tissue types including root, leaf, petal, and kernel. Further investigation revealed that Vf/VmLRR-RLK orthologous genes mainly showed similar expression patterns in response to tree wilt disease, except 4 pairs of Vf/VmLRR-RLKs that showed opposite expression trends. These results represent an extensive evaluation of LRR-RLKs in two industrial oil trees and will be useful for further functional studies on these proteins. Huiping Zhu, Yangdong Wang, Hengfu Yin, Ming Gao, Qiyan Zhang, and Yicun Chen Copyright © 2015 Huiping Zhu et al. All rights reserved. Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication Mon, 07 Dec 2015 14:09:01 +0000 The basic leucine zipper (bZIP) transcription factors are the most diverse members of dimerizing transcription factors. In the present study, 50, 116, and 47 bZIP genes were identified in Malus domestica (apple), Prunus persica (peach), and Fragaria vesca (strawberry), respectively. Species-specific duplication was the main contributor to the large number of bZIPs observed in apple. After WGD in apple genome, orthologous bZIP genes corresponding to strawberry on duplicated regions in apple genome were retained. However, in peach ancestor, these syntenic regions were quickly lost or deleted. Maybe the positive selection contributed to the expansion of clade S to adapt to the development and environment stresses. In addition, purifying selection was mainly responsible for bZIP sequence-specific DNA binding. The analysis of orthologous pairs between chromosomes indicates that these orthologs derived from one gene duplication located on one of the nine ancient chromosomes in the Rosaceae. The comparative analysis of bZIP genes in three species provides information on the evolutionary fate of bZIP genes in apple and peach after they diverged from strawberry. Xiao-Long Wang, Yan Zhong, Zong-Ming Cheng, and Jin-Song Xiong Copyright © 2015 Xiao-Long Wang et al. All rights reserved. De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome Tue, 24 Nov 2015 14:22:42 +0000 The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR. Vladimir A. Zhukov, Alexander I. Zhernakov, Olga A. Kulaeva, Nikita I. Ershov, Alexey Y. Borisov, and Igor A. Tikhonovich Copyright © 2015 Vladimir A. Zhukov et al. All rights reserved. Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.) Thu, 19 Nov 2015 13:06:04 +0000 Perilla frutescens is valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses of P. frutescens are limited due to a lack of gene annotations and characterization. A full-length cDNA library from P. frutescens leaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers from P. frutescens will help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant. Eun Soo Seong, Ji Hye Yoo, Jae Hoo Choi, Chang Heum Kim, Mi Ran Jeon, Byeong Ju Kang, Jae Geun Lee, Seon Kang Choi, Bimal Kumar Ghimire, and Chang Yeon Yu Copyright © 2015 Eun Soo Seong et al. All rights reserved. De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis Sun, 15 Nov 2015 13:07:50 +0000 Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop worldwide. The orange-fleshed sweet potato is considered to be an important source of beta-carotene. In this study, the transcriptome profiles of an orange-fleshed sweet potato cultivar “Weiduoli” and its mutant “HVB-3” with high carotenoid content were determined by using the high-throughput sequencing technology. A total of 13,767,387 and 9,837,090 high-quality reads were produced from Weiduoli and HVB-3, respectively. These reads were de novo assembled into 58,277 transcripts and 35,909 unigenes with an average length of 596 bp and 533 bp, respectively. In all, 874 differentially expressed genes (DEGs) were obtained between Weiduoli and HVB-3, 401 of which were upregulated and 473 were downregulated in HVB-3 compared to Weiduoli. Of the 697 DEGs annotated, 316 DEGs had GO terms and 62 DEGs were mapped onto 50 pathways. The 22 DEGs and 31 transcription factors involved in carotenoid biosynthesis were identified between Weiduoli and HVB-3. In addition, 1,725 SSR markers were detected. This study provides the genomic resources for discovering the genes involved in carotenoid biosynthesis of sweet potato and other plants. Ruijie Li, Hong Zhai, Chen Kang, Degao Liu, Shaozhen He, and Qingchang Liu Copyright © 2015 Ruijie Li et al. All rights reserved. Quantitative Shotgun Proteomics Analysis of Rice Anther Proteins after Exposure to High Temperature Thu, 05 Nov 2015 12:45:31 +0000 In rice, the stage of development most sensitive to high temperature stress is flowering, and exposure at this stage can result in spikelet sterility, thereby leading to significant yield losses. In this study, protein expression patterns of rice anthers from Dianxi4, a high temperature tolerant Japonica rice variety, were compared between samples exposed to high temperature and those grown in natural field conditions in Korea. Shotgun proteomics analysis of three replicate control and high-temperature-treated samples identified 3,266 nonredundant rice anther proteins (false discovery rate < 0.01). We found that high levels of ATP synthase, cupin domain-containing proteins, and pollen allergen proteins were present in rice anthers. Comparative analyses of 1,944 reproducibly expressed proteins identified 139 differentially expressed proteins, with 95 increased and 44 decreased in response to high temperature conditions. Heat shock, DnaK family, and chaperone proteins showed highly increased expression, suggesting that the high temperature tolerance of Dianxi4 is achieved by stabilization of proteins in pollen cells. Trehalose synthase was also highly increased after heat treatment, suggesting a possible role for trehalose in preventing protein denaturation through desiccation. Mijeong Kim, Hijin Kim, Wondo Lee, Yoonjung Lee, Soon-Wook Kwon, and Joohyun Lee Copyright © 2015 Mijeong Kim et al. All rights reserved. Identification of Immune Related LRR-Containing Genes in Maize (Zea mays L.) by Genome-Wide Sequence Analysis Thu, 22 Oct 2015 07:52:58 +0000 A large number of immune receptors consist of nucleotide binding site-leucine rich repeat (NBS-LRR) proteins and leucine rich repeat-receptor-like kinases (LRR-RLK) that play a crucial role in plant disease resistance. Although many NBS-LRR genes have been previously identified in Zea mays, there are no reports on identifying NBS-LRR genes encoded in the N-terminal Toll/interleukin-1 receptor (TIR) motif and identifying genome-wide LRR-RLK genes. In the present study, 151 NBS-LRR genes and 226 LRR-RLK genes were identified after performing bioinformatics analysis of the entire maize genome. Of these identified genes, 64 NBS-LRR genes and four TIR-NBS-LRR genes were identified for the first time. The NBS-LRR genes are unevenly distributed on each chromosome with gene clusters located at the distal end of each chromosome, while LRR-RLK genes have a random chromosomal distribution with more paired genes. Additionally, six LRR-RLK/RLPs including FLS2, PSY1R, PSKR1, BIR1, SERK3, and Cf5 were characterized in Zea mays for the first time. Their predicted amino acid sequences have similar protein structures with their respective homologues in other plants, indicating that these maize LRR-RLK/RLPs have the same functions as their homologues act as immune receptors. The identified gene sequences would assist in the study of their functions in maize. Wei Song, Baoqiang Wang, Xinghua Li, Jianfen Wei, Ling Chen, Dongmin Zhang, Wenying Zhang, and Ronggai Li Copyright © 2015 Wei Song et al. All rights reserved. Novel Computational Technologies for Next-Generation Sequencing Data Analysis and Their Applications Tue, 20 Oct 2015 13:51:29 +0000 Chuan Yi Tang, Che-Lun Hung, Huiru Zheng, Chun-Yuan Lin, and Hai Jiang Copyright © 2015 Chuan Yi Tang et al. All rights reserved. Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency Mon, 19 Oct 2015 11:52:56 +0000 Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB. Rodrigo Aniceto, Rene Xavier, Valeria Guimarães, Fernanda Hondo, Maristela Holanda, Maria Emilia Walter, and Sérgio Lifschitz Copyright © 2015 Rodrigo Aniceto et al. All rights reserved. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes Mon, 19 Oct 2015 09:10:16 +0000 Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software. Krisztian Buza, Bartek Wilczynski, and Norbert Dojer Copyright © 2015 Krisztian Buza et al. All rights reserved. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System Mon, 19 Oct 2015 07:49:36 +0000 The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively. Yu Liu, Yang Hong, Chun-Yuan Lin, and Che-Lun Hung Copyright © 2015 Yu Liu et al. All rights reserved. A New Binning Method for Metagenomics by One-Dimensional Cellular Automata Sun, 18 Oct 2015 12:20:46 +0000 More and more developed and inexpensive next-generation sequencing (NGS) technologies allow us to extract vast sequence data from a sample containing multiple species. Characterizing the taxonomic diversity for the planet-size data plays an important role in the metagenomic studies, while a crucial step for doing the study is the binning process to group sequence reads from similar species or taxonomic classes. The metagenomic binning remains a challenge work because of not only the various read noises but also the tremendous data volume. In this work, we propose an unsupervised binning method for NGS reads based on the one-dimensional cellular automaton (1D-CA). Our binning method facilities to reduce the memory usage because 1D-CA costs only linear space. Experiments on synthetic dataset exhibit that our method is helpful to identify species of lower abundance compared to the proposed tool. Ying-Chih Lin Copyright © 2015 Ying-Chih Lin. All rights reserved. SimpLiFiCPM: A Simple and Lightweight Filter-Based Algorithm for Circular Pattern Matching Sun, 18 Oct 2015 12:14:25 +0000 This paper deals with the circular pattern matching (CPM) problem, which appears as an interesting problem in many biological contexts. CPM consists in finding all occurrences of the rotations of a pattern of length in a text of length . In this paper, we present SimpLiFiCPM (pronounced “Simplify CPM”), a simple and lightweight filter-based algorithm to solve the problem. We compare our algorithm with the state-of-the-art algorithms and the results are found to be excellent. Much of the speed of our algorithm comes from the fact that our filters are effective but extremely simple and lightweight. Md. Aashikur Rahman Azim, Costas S. Iliopoulos, M. Sohel Rahman, and M. Samiruzzaman Copyright © 2015 Md. Aashikur Rahman Azim et al. 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.