International Journal of Genomics The latest articles from Hindawi Publishing Corporation © 2016 , Hindawi Publishing Corporation . All rights reserved. GPA-MDS: A Visualization Approach to Investigate Genetic Architecture among Phenotypes Using GWAS Results Thu, 27 Oct 2016 11:38:54 +0000 Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. Recently, there has been accumulating evidence suggesting that different complex traits share a common risk basis, namely, pleiotropy. Previously, a statistical method, namely, GPA (Genetic analysis incorporating Pleiotropy and Annotation), was developed to improve identification of risk variants and to investigate pleiotropic structure through a joint analysis of multiple GWAS datasets. While GPA provides a statistically rigorous framework to evaluate pleiotropy between phenotypes, it is still not trivial to investigate genetic relationships among a large number of phenotypes using the GPA framework. In order to address this challenge, in this paper, we propose a novel approach, GPA-MDS, to visualize genetic relationships among phenotypes using the GPA algorithm and multidimensional scaling (MDS). This tool will help researchers to investigate common etiology among diseases, which can potentially lead to development of common treatments across diseases. We evaluate the proposed GPA-MDS framework using a simulation study and apply it to jointly analyze GWAS datasets examining 18 unique phenotypes, which helps reveal the shared genetic architecture of these phenotypes. Wei Wei, Paula S. Ramos, Kelly J. Hunt, Bethany J. Wolf, Gary Hardiman, and Dongjun Chung Copyright © 2016 Wei Wei et al. All rights reserved. Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster, Pinctada fucata, Based on Transcriptome Analysis Sun, 23 Oct 2016 07:38:51 +0000 P. fucata experiences a series of transformations in appearance, from swimming larvae to sessile juveniles, during which significant changes in gene expression likely occur. Thus, P. fucata could be an ideal model in which to study the molecular mechanisms of larval metamorphosis during development in invertebrates. To study the molecular driving force behind metamorphic development in larvae of P. fucata, transcriptomes of five larval stages (trochophore, D-shape, umbonal, eyespots, and spats) were sequenced using an Illumina HiSeq™ 2000 system and assembled and characterized with the transcripts of six tissues. As a result, a total of 174,126 unique transcripts were assembled and 60,999 were annotated. The number of unigenes varied among the five larval stages. Expression profiles were distinctly different between trochophore, D-shape, umbonal, eyespots, and spats larvae. As a result, 29 expression trends were sorted, of which eight were significant. Among others, 80 development-related, differentially expressed unigenes (DEGs) were identified, of which the majority were homeobox-containing genes. Most DEGs occurred among trochophore, D-shaped, and UES (umbonal, eyespots, and spats) larvae as verified by qPCR. Principal component analysis (PCA) also revealed significant differences in expression among trochophore, D-shaped, and UES larvae with ten transcripts identified but no matching annotations. Haimei Li, Bo Zhang, Guiju Huang, Baosuo Liu, Sigang Fan, Dongling Zhang, and Dahui Yu Copyright © 2016 Haimei Li et al. All rights reserved. Proteome Analysis of Date Palm (Phoenix dactylifera L.) under Severe Drought and Salt Stress Thu, 20 Oct 2016 09:31:31 +0000 Date palm cultivars differently tolerate salinity and drought stress. This study was carried out to study the response of date palm to severe salinity and drought based on leaf proteome analysis. Eighteen-month-old date palm plants were subjected to severe salt (48 g/L NaCl) and drought (82.5 g/L PEG or no irrigation) conditions for one month. Using a protein 2D electrophoresis method, 55 protein spots were analyzed using mass spectrometry. ATP synthase CF1 alpha chains were significantly upregulated under all three stress conditions. Changes in the abundance of RubisCO activase and one of the RubisCO fragments were significant in the same spots only for salt stress and drought stress with no irrigation, and oxygen-evolving enhancer protein 2 was changed in different spots. Transketolase was significantly changed only in drought stress with PEG. The expression of salt and drought stress genes of the chosen protein spots was either overexpressed or downexpressed as revealed by the high or low protein abundance, respectively. In addition, all drought tolerance genes due to no irrigation were downregulated. In conclusion, the proteome analysis of date palm under salinity and drought conditions indicated that both salinity and drought tolerance genes were differentially expressed resulting in high or low protein abundance of the chosen protein spots as a result of exposure to drought and salinity stress condition. Haddad A. El Rabey, Abdulrahman L. Al-Malki, and Khalid O. Abulnaja Copyright © 2016 Haddad A. El Rabey et al. All rights reserved. Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway Sun, 16 Oct 2016 11:33:41 +0000 Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis. John J. Wilson, Janelle Grendler, Azaline Dunlap-Smith, Brian F. Beal, and Shallee T. Page Copyright © 2016 John J. Wilson et al. All rights reserved. Performance Characterization and Validation of Saliva as an Alternative Specimen Source for Detecting Hereditary Breast Cancer Mutations by Next Generation Sequencing Thu, 13 Oct 2016 13:33:32 +0000 Identification of pathogenic germline mutations by next generation sequencing is a widely accepted tool for predicting the risk of hereditary cancer development. Blood is the most common source of DNA for such tests. However, blood as a sample type has many drawbacks, including the invasive collection method, poor sample stability, and a relatively high cost of collection. Therefore, in the current study we have assessed the suitability of saliva as an alternative source of genomic DNA for the identification of germline mutations in the BRCA1/2 genes by next generation sequencing (NGS). Our results show that all of the samples yielded DNA concentrations sufficient for library preparation. The concentrations of the final libraries, which were generated by PCR using target specific primers, fall into the expected range with no notable difference between libraries generated from DNA derived from saliva or blood. Quality parameters indicate that sequencing performance is comparable across sample source. An average of ()% variant calling concordance was obtained between the two specimen sources. Our data recommends saliva as a potential alternative for detecting germline mutation by next generation sequencing. Varsha Meghnani, Nadeem Mohammed, Christopher Giauque, Rahul Nahire, and Thomas David Copyright © 2016 Varsha Meghnani et al. All rights reserved. Molecular Cloning, Characterization, and mRNA Expression of Hemocyanin Subunit in Oriental River Prawn Macrobrachium nipponense Thu, 13 Oct 2016 12:47:07 +0000 Hemocyanin is a copper-containing protein with immune function against disease. In this study, a hemocyanin subunit named MnHc-1 was cloned from Macrobrachium nipponense. The full-length cDNA of MnHc-1 was 2,163 bp with a 2,028-bp open reading frame (ORF) encoding a polypeptide of 675 amino acids. The MnHc-1 mRNA was expressed in the hepatopancreas, gill, hemocytes, intestine, ovary, and stomach, with the highest level in the hepatopancreas. In the infection trial, the MnHc-1 mRNA transcripts in the hemocytes were significantly downregulated at 3 h after injection of Aeromonas hydrophila and then upregulated at 6 h and 12 h, followed by a gradual recovery from 24 to 48 h. The MnHc-1 transcriptional expression in the hepatopancreas was measured after M. nipponense were fed seven diets with 2.8, 12.2, 20.9, 29.8, 43.1, 78.9, and 157.1 mg Cu kg−1 for 8 weeks, respectively. The level of MnHc-1 mRNA was significantly higher in the prawns fed 43.1–157.1 mg Cu kg−1 diet than in that fed 2.8–29.8 mg Cu kg−1 diet. This study indicated that the MnHc-1 expression can be affected by dietary copper and the hemocyanin may potentially participate in the antibacterial defense of M. nipponense. Youqin Kong, Liqiao Chen, Zhili Ding, Jianguang Qin, Shengming Sun, Ligai Wang, and Jinyun Ye Copyright © 2016 Youqin Kong et al. All rights reserved. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining Wed, 28 Sep 2016 13:55:34 +0000 Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (). We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates. We found that the RNase H method produced higher quality RNAseq data as compared to the Ribo-Zero method. In addition, we evaluated the RNAseq data generated from the FFPE tissue samples for noncoding RNA, including lncRNA, enhancer/super enhancer RNA, and single nucleotide variation (SNV). We found that the RNase H is more suitable for detecting high-quality, noncoding RNAs as compared to the Ribo-Zero and provided more consistent molecular subtype identification between replicates. Unfortunately, neither method produced reliable SNV data. Conclusions. In conclusion, for FFPE specimens, the RNase H rRNA depletion method performed better than the Ribo-Zero. Neither method generates data sufficient for SNV detection. Yan Guo, Jie Wu, Shilin Zhao, Fei Ye, Yinghao Su, Travis Clark, Quanhu Sheng, Brian Lehmann, Xiao-ou Shu, and Qiuyin Cai Copyright © 2016 Yan Guo et al. All rights reserved. Embracing Integrative Multiomics Approaches Sun, 04 Sep 2016 09:38:55 +0000 As “-omics” data technology advances and becomes more readily accessible to address complex biological questions, increasing amount of cross “-omics” dataset is inspiring the use and development of integrative bioinformatics analysis. In the current review, we discuss multiple options for integrating data across “-omes” for a range of study designs. We discuss established methods for such analysis and point the reader to in-depth discussions for the various topics. Additionally, we discuss challenges and new directions in the area. Daniel M. Rotroff and Alison A. Motsinger-Reif Copyright © 2016 Daniel M. Rotroff and Alison A. Motsinger-Reif. All rights reserved. Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family in Gossypium Wed, 31 Aug 2016 07:50:32 +0000 Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated in Arabidopsis and rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified in Gossypium arboreum and Gossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are distributed across 7 chromosomes in Gossypium arboreum and 8 chromosomes in Gossypium raimondii. Segmental duplication is predominant duplication event and major contributor for expansion of SOD gene family. Gene structure and protein structure analysis showed that SOD genes have conserved exon/intron arrangement and motif composition. Microarray-based expression analysis revealed that SOD genes have important function in abiotic stress. Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. Taken together, this study has imparted new insights into the putative functions of SOD gene family in cotton. Findings of the present investigation could help in understanding the role of SOD gene family in various aspects of the life cycle of cotton. Jingbo Zhang, Bo Li, Yang Yang, Wenran Hu, Fangyuan Chen, Lixia Xie, and Ling Fan Copyright © 2016 Jingbo Zhang et al. All rights reserved. Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine Tue, 30 Aug 2016 15:36:33 +0000 Monitoring disease activity in a complex, heterogeneous disease such as lupus is difficult. Both over- and undertreatment lead to damage. Current standard of care serologies are unreliable. Better measures of disease activity are necessary as we move into the era of precision medicine. We show here the use of a data-driven, modular approach to genomic biomarker development within lupus—specifically lupus nephritis. Eric Zollars, Sean M. Courtney, Bethany J. Wolf, Norm Allaire, Ann Ranger, Gary Hardiman, and Michelle Petri Copyright © 2016 Eric Zollars et al. All rights reserved. Genetic Contribution of Ningmai 9 Wheat to Its Derivatives Evaluated by Using SNP Markers Mon, 29 Aug 2016 14:32:22 +0000 Founder parent usually plays an important role in wheat breeding. Ningmai 9 is a soft wheat variety with good performance in yield, quality, and resistance to wheat disease. Therefore it serves as an important commercial variety and founder parent in middle and lower Yangtze River of China. To date, 20 new cultivars have been developed from Ningmai 9 and released to wheat production in the last 10 years. In this study, the 90K iSELECT ILLUMINA chip was used to analyze the genotype of Ningmai 9 and its 17 derivatives. The genetic similarity coefficients between Ningmai 9 and its derivatives were more than 0.7 except for Yangfumai 4. Neighbor-Joining analysis showed that Yangfumai 4 had the largest genetic distance from Ningmai 9 in all derivatives. There was a great difference for the same allele ratio in either derivatives or chromosomes, though the average values of the same allele ratio in genomes A, B, and D were close to each other. The phenotypic difference in Ningmai 9, Ningmai 13, and Yangfumai 4 was consistent with their difference in genetic background by comparing previous reported QTLs. Some hot chromosome regions were found and might be used for marker assisted selection in wheat breeding. Peng Jiang, Ping-Ping Zhang, Xu Zhang, and Hong-Xiang Ma Copyright © 2016 Peng Jiang et al. All rights reserved. Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss) Mon, 29 Aug 2016 09:21:11 +0000 Excessive accumulation of carcass fat in farm animals, including fish, has a significant impact on meat quality and on the cost of feeding. Similar to farmed animals and humans, the liver can be considered one of the most important organs involved in lipid metabolism in rainbow trout (Oncorhynchus mykiss). RNA-seq based whole transcriptome sequencing was performed to liver tissue of rainbow trout with high and low carcass fat content in this study. In total 1,694 differentially expressed transcripts were identified, including many genes involved in lipid metabolism, such as L-FABP, adiponectin, PPAR-α, PPAR-β, and IGFBP1a. Evidence presented in this study indicated that lipid metabolic process in liver may be related to the difference of carcass fat content. The relevance of PPAR-α and PPAR-β as molecular markers for fat storage in liver should be worthy of further investigation. Guo Hu, Wei Gu, Peng Sun, Qingli Bai, and Bingqian Wang Copyright © 2016 Guo Hu et al. All rights reserved. Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress Thu, 18 Aug 2016 11:22:07 +0000 Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions. Ha Duc Chu, Quynh Ngoc Le, Huy Quang Nguyen, and Dung Tien Le Copyright © 2016 Ha Duc Chu et al. All rights reserved. Histological and Molecular Characterization of Grape Early Ripening Bud Mutant Wed, 17 Aug 2016 06:07:17 +0000 An early ripening bud mutant was analyzed based on the histological, SSR, and methylation-sensitive amplified polymorphism (MSAP) analysis and a layer-specific approach was used to investigate the differentiation between the bud mutant and its parent. The results showed that the thickness of leaf spongy tissue of mutant (MT) is larger than that of wild type (WT) and the differences are significant. The mean size of cell layer L2 was increased in the mutant and the difference is significant. The genetic background of bud mutant revealed by SSR analysis is highly uniform to its parent; just the variations from VVS2 SSR marker were detected in MT. The total methylation ratio of MT is lower than that of the corresponding WT. The outside methylation ratio in MT is much less than that in WT; the average inner methylation ratio in MT is larger than that in WT. The early ripening bud mutant has certain proportion demethylation in cell layer L2. All the results suggested that cell layer L2 of the early ripening bud mutant has changed from the WT. This study provided the basis for a better understanding of the characteristic features of the early ripening bud mutant in grape. Da-Long Guo, Yi-He Yu, Fei-Fei Xi, Yan-Yan Shi, and Guo-Hai Zhang Copyright © 2016 Da-Long Guo et al. All rights reserved. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India Mon, 25 Jul 2016 16:04:34 +0000 Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis. Sarwar Azam, Sashi Bhushan Rao, Padmaja Jakka, Veera NarasimhaRao, Bindu Bhargavi, Vivek Kumar Gupta, and Girish Radhakrishnan Copyright © 2016 Sarwar Azam et al. All rights reserved. SSR Mapping of QTLs Conferring Cold Tolerance in an Interspecific Cross of Tomato Tue, 19 Jul 2016 12:49:36 +0000 A population of 146 RILs (Recombinant Inbred Line) was derived from the cross between a cold-sensitive cultivated Solanum lycopersicum L. XF98-7 and a cold-tolerant wild Solanum pimpinellifolium LA2184. Relative germination ratio (RGR) and chilling index (CI) were used to evaluate the cold tolerance of the parental lines and RILs. It was found that the RGR and CI were significantly different between S. lycopersicum XF98-7 and S. pimpinellifolium LA2184 under cold treatment, indicating that wild species was more adapted to chilling temperature. The continuous and normal distribution of RGR and CI in RIL population suggested that the trait of cold tolerance was a typically quantitative trait controlled by multigenes. The molecular linkage map was constructed by using 120 simple-sequence repeat (SSR) markers, resulting in 15 linkage groups, with a total distance of 256.8 cM and average interval of 2.14 cM. Five QTLs controlling RGR and four QTLs for CI were detected with genetic contribution ranging from 0.95% to 19.55%. Thus, the nine QTLs will provide references for further fine position mapping for cold tolerance. The polymorphic markers could be used as a way of indirectly selecting the plant trait of interest and would promote developing new tomato variety by marker-assisted selection. Yang Liu, Tengxia Zhou, Haiyan Ge, Wen Pang, Lijie Gao, Li Ren, and Huoying Chen Copyright © 2016 Yang Liu et al. All rights reserved. Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology Wed, 13 Jul 2016 07:36:42 +0000 Cancerlectins are cancer-related proteins that function as lectins. They have been identified through computational identification techniques, but these techniques have sometimes failed to identify proteins because of sequence diversity among the cancerlectins. Advanced machine learning identification methods, such as support vector machine and basic sequence features (n-gram), have also been used to identify cancerlectins. In this study, various protein fingerprint features and advanced classifiers, including ensemble learning techniques, were utilized to identify this group of proteins. We improved the prediction accuracy of the original feature extraction methods and classification algorithms by more than 10% on average. Our work provides a basis for the computational identification of cancerlectins and reveals the power of hybrid machine learning techniques in computational proteomics. Jieru Zhang, Ying Ju, Huijuan Lu, Ping Xuan, and Quan Zou Copyright © 2016 Jieru Zhang et al. All rights reserved. De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.) Mon, 27 Jun 2016 14:20:29 +0000 Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome of T. turgidum, 56,343 unigenes were matched with 103,327 unigenes of T. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed. Yi Wang, Chao Wang, Xiaolu Wang, Fan Peng, Ruijiao Wang, Yulin Jiang, Jian Zeng, Xing Fan, Houyang Kang, Lina Sha, Haiqin Zhang, Xue Xiao, and Yonghong Zhou Copyright © 2016 Yi Wang et al. All rights reserved. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.) Wed, 22 Jun 2016 09:01:26 +0000 The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. Gyu-Ho Lee, In-Kyu Kang, and Kyung-Min Kim Copyright © 2016 Gyu-Ho Lee et al. All rights reserved. Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line “Chiifu”) Tue, 21 Jun 2016 09:54:49 +0000 Through a comparative shotgun quantitative proteomics analysis in Brassica rapa (inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein. Soon-Wook Kwon, Mijeong Kim, Hijin Kim, and Joohyun Lee Copyright © 2016 Soon-Wook Kwon et al. All rights reserved. Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile Mon, 20 Jun 2016 14:38:06 +0000 Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories in Nothofagus dombeyi requires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species. Rodrigo Hasbún, Jorge González, Carolina Iturra, Glenda Fuentes, Diego Alarcón, and Eduardo Ruiz Copyright © 2016 Rodrigo Hasbún et al. All rights reserved. Drug Target Identification and Prioritization for Treatment of Ovine Foot Rot: An In Silico Approach Thu, 09 Jun 2016 08:38:35 +0000 Ovine foot rot is an infection of the feet of sheep, mainly caused by Dichelobacter nodosus. In its virulent form, it is highly contagious and debilitating, causing significant losses in the form of decline in wool growth and quality and poor fertility. Current methods of treatment are ineffective in complete eradication. Effective antibiotic treatment of foot rot is hence necessary to ensure better outcomes during control phases by reduction in culling count and the possibility of carriers of the infection. Using computational approaches, we have identified a set of 297 proteins that are essential to the D. nodosus and nonhomologous with sheep proteins. These proteins may be considered as potential vaccine candidates or drug targets for designing antibiotics against the bacterium. This core set of drug targets have been analyzed for pathway annotation to identify 67 proteins involved in unique bacterial pathways. Choke-point analysis on the drug targets identified 138 choke-point proteins, 29 involved in unique bacterial pathways. Subcellular localization was also predicted for each target to identify the ones that are membrane associated or secreted extracellularly. In addition, a total of 13 targets were identified that are common in at least 10 pathogenic bacterial species. Abhishek Acharya and Lalit C. Garg Copyright © 2016 Abhishek Acharya and Lalit C. Garg. All rights reserved. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species Wed, 08 Jun 2016 08:30:37 +0000 Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management. Kristopher J. L. Irizarry, Doug Bryant, Jordan Kalish, Curtis Eng, Peggy L. Schmidt, Gini Barrett, and Margaret C. Barr Copyright © 2016 Kristopher J. L. Irizarry et al. All rights reserved. De Novo Assembly and Comparative Transcriptome Analysis Provide Insight into Lysine Biosynthesis in Toona sinensis Roem Tue, 07 Jun 2016 12:18:10 +0000 Toona sinensis Roem is a popular leafy vegetable in Chinese cuisine and is also used as a traditional Chinese medicine. In this study, leaf samples were collected from the same plant on two development stages and then used for high-throughput Illumina RNA-sequencing (RNA-Seq). 125,884 transcripts and 54,628 unigenes were obtained through de novo assembly. A total of 25,570 could be annotated with known biological functions, which indicated that the T. sinensis leaves and shoots were undergoing multiple developmental processes especially for active metabolic processes. Analysis of differentially expressed unigenes between the two libraries showed that the lysine biosynthesis was an enriched KEGG pathway, and candidate genes involved in the lysine biosynthesis pathway in T. sinensis leaves and shoots were identified. Our results provide a primary analysis of the gene expression files of T. sinensis leaf and shoot on different development stages and afford a valuable resource for genetic and genomic research on plant lysine biosynthesis. Xia Zhang, Zhenqiao Song, Tian Liu, Linlin Guo, and Xingfeng Li Copyright © 2016 Xia Zhang et al. All rights reserved. Comparative Genomics of Herpesviridae Family to Look for Potential Signatures of Human Infecting Strains Thu, 26 May 2016 07:59:47 +0000 Herpesviridae family is one of the significant viral families which comprises major pathogens of a wide range of hosts. This family includes at least eight species of viruses which are known to infect humans. This family has evolved 180–220 million years ago and the present study highlights that it is still evolving and more genes can be added to the repertoire of this family. In addition, its core-genome includes important viral proteins including glycoprotein B and helicase. Most of the infections caused by human herpesviruses have no definitive cure; thus, search for new therapeutic strategies is necessary. The present study finds core-genome of human herpesviruses that differs from that of Herpesviridae family and nonhuman herpes strains of this family and might be a putative target for vaccine development. The phylogenetic reconstruction based upon the protein sequences of core gene set of Herpesviridae family reveals the sharp splits of its different subfamilies and supports the hypothesis of coevolution of viruses with their hosts. In addition, data mining for cis-elements in the genomes of human herpesviruses results in the prediction of numerous regulatory elements which can be used for regulating the expression of viral based vectors implicated in gene therapies. Vikas Sharma, Fauzul Mobeen, and Tulika Prakash Copyright © 2016 Vikas Sharma et al. All rights reserved. Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment Thu, 12 May 2016 14:21:30 +0000 Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs). The results show that light bands are preferential targets for integration of HIV-1 in Jurkat cells and also that it integrates with equal intensity in FSs and in NFSs. The data indicates that HIV displays different preferences for FSs compared to other viruses. The aim was to develop and apply an approach to predict the conditions and constraints of HIV insertion in the human genome which seems to adequately complement empirical data. Juliana Gonçalves, Elsa Moreira, Inês J. Sequeira, António S. Rodrigues, José Rueff, and Aldina Brás Copyright © 2016 Juliana Gonçalves et al. All rights reserved. A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population Tue, 19 Apr 2016 13:03:34 +0000 The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics. Palle Duun Rohde, Kristian Krag, Volker Loeschcke, Johannes Overgaard, Peter Sørensen, and Torsten Nygaard Kristensen Copyright © 2016 Palle Duun Rohde et al. All rights reserved. The Microbiome of Animals: Implications for Conservation Biology Mon, 18 Apr 2016 13:40:33 +0000 In recent years the human microbiome has become a growing area of research and it is becoming clear that the microbiome of humans plays an important role for human health. Extensive research is now going into cataloging and annotating the functional role of the human microbiome. The ability to explore and describe the microbiome of any species has become possible due to new methods for sequencing. These techniques allow comprehensive surveys of the composition of the microbiome of nonmodel organisms of which relatively little is known. Some attention has been paid to the microbiome of insect species including important vectors of pathogens of human and veterinary importance, agricultural pests, and model species. Together these studies suggest that the microbiome of insects is highly dependent on the environment, species, and populations and affects the fitness of species. These fitness effects can have important implications for the conservation and management of species and populations. Further, these results are important for our understanding of invasion of nonnative species, responses to pathogens, and responses to chemicals and global climate change in the present and future. Simon Bahrndorff, Tibebu Alemu, Temesgen Alemneh, and Jeppe Lund Nielsen Copyright © 2016 Simon Bahrndorff et al. All rights reserved. Transcriptomic Analysis of Resistant and Susceptible Bombyx mori Strains Following BmNPV Infection Provides Insights into the Antiviral Mechanisms Mon, 18 Apr 2016 07:33:11 +0000 Purpose. To decipher transcriptomic changes and related genes with potential functions against Bombyx mori nucleopolyhedrovirus infection and to increase the understanding of the enhanced virus resistance of silkworm on the transcriptomic level. Methods. We assembled and annotated transcriptomes of the Qiufeng (susceptible to infection) and QiufengN (resistant to infection) strains and performed comparative analysis in order to decipher transcriptomic changes and related genes with potential functions against BmNPV infection. Results. A total of 78,408 SNPs were identified in the Qiufeng strain of silkworm and 56,786 SNPs were identified in QiufengN strain. Besides, novel AS events were found in these 2 strains. In addition, 1,728 DEGs were identified in the QiufengN strain compared with Qiufeng strain. These DEGs were involved in GO terms related to membrane, metabolism, binding and catalytic activity, cellular processes, and organismal systems. The highest levels of gene representation were found in oxidative phosphorylation, phagosome, TCA cycle, arginine and proline metabolism, and pyruvate metabolism. Additionally, COG analysis indicated that DEGs were involved in “amino acid transport and metabolism” and “carbohydrate transport and metabolism.” Conclusion. We identified a series of major pathological changes in silkworm following infection and several functions were related to the antiviral mechanisms of silkworm. Gang Li, Heying Qian, Xufang Luo, Pingzhen Xu, Jianhua Yang, Mingzhu Liu, and Anying Xu Copyright © 2016 Gang Li et al. All rights reserved. The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer) Mitochondrion Mon, 11 Apr 2016 06:49:53 +0000 The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants. Xuelin Wang, Changwei Bi, Yiqing Xu, Suyun Wei, Xiaogang Dai, Tongming Yin, and Ning Ye Copyright © 2016 Xuelin Wang et al. All rights reserved.