Plant Biology Commons^™

Wheat Streak Mosaic Virus Infects Systemically Despite Extensive Coat Protein Deletions: Identification Of Virion Assembly And Cell-To-Cell Movement Determinants, Satyanarayana Tatineni, Frank A. Kovacs, Roy C. French

Department of Plant Pathology: Faculty Publications

Viral coat proteins function in virion assembly and virus biology in a tightly coordinated manner with a role for virtually every amino acid. In this study, we demonstrated that the coat protein (CP) of Wheat streak mosaic virus (WSMV) (genus Tritimovirus; family Potyviridae) is unusually tolerant of extensive deletions with continued virion assembly and/or systemic infection. A series of deletion and point mutations were created in the CP cistron of wild-type and/or GFP-tagged WSMV and examined the effects of these mutations on cell-to-cell and systemic transport and virion assembly of WSMV. Mutants with overlapping deletions comprising N-terminal amino …

Calmodulin-Mediated Signal Transduction Pathways In Arabidopsis Are Fine-Tuned By Methylation, Joydeep Banerjee, Roberta Magnani, Meera Nair, Lynnette M. Dirk, Seth Debolt, Indu B. Maiti, Robert L. Houtz

Department of Plant Pathology: Faculty Publications

Calmodulin N-methyltransferase (CaM KMT) is an evolutionarily conserved enzyme in eukaryotes that transfers three methyl groups to a highly conserved lysyl residue at position 115 in calmodulin (CaM). We sought to elucidate whether the methylation status of CaM plays a role in CaM-mediated signaling pathways by gene expression analyses of CaM KMT and phenotypic characterization of Arabidopsis thaliana lines wherein CaM KMT was overexpressed (OX), partially silenced, or knocked out. CaM KMT was expressed in discreet spatial and tissue-specific patterns, most notably in root tips, floral buds, stamens, apical meristems, and germinating seeds. Analysis of transgenic plants with genetic dysfunction …

Quantitative Relationship Of Soil Texture With The Observed Population Density Reduction Of Heterodera Glycines After Annual Corn Rotation In Nebraska, Oscar Perez-Hernandez, Loren J. Giesler

Department of Plant Pathology: Faculty Publications

Soil texture has been commonly associated with the population density of Heterodera glycines (soybean cyst nematode: SCN), but such an association has been mainly described in terms of textural classes. In this study, multivariate analysis and a generalized linear modeling approach were used to elucidate the quantitative relationship of soil texture with the observed SCN population density reduction after annual corn rotation in Nebraska. Forty-five commercial production fields were sampled in 2009, 2010, and 2011 and SCN population density (eggs/100 cm3 of soil) for each field was determined before (Pi) and after (Pf) annual corn rotation from ten 3 3 …

Metagenomic Profiling Reveals Lignocellulose Degrading System In A Microbial Community Associated With A Wood-Feeding Beetle, Erin D. Scully, Scott M. Geib, Kelli Hoover, Ming Tien, Susannah G. Tringe, Kerrie W. Barry, Tijana Glavina Del Rio, Mansi Chovatia, Joshua R. Herr, John E. Carlson

Department of Plant Pathology: Faculty Publications

The Asian longhorned beetle (Anoplophora glabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little …

Dynamic Expression Of Imprinted Genes Associates With Maternally Controlled Nutrient Allocation During Maize Endosperm Development, Mingming Xin, Ruolin Yang, Guosheng Li, Hao Chen, John Laurie, Chuang Ma, Dongfang Wang, Yingyin Yao, Brian A. Larkins, Qixin Sun, Ramin Yadegari, Xiangfeng Wang, Zhongfu Ni

Center for Plant Science Innovation: Faculty Publications

In angiosperms, the endosperm provides nutrients for embryogenesis and seed germination and is the primary tissue where gene imprinting occurs. To identify the imprintome of early developing maize (Zea mays) endosperm, we performed highthroughput transcriptome sequencing of whole kernels at 0, 3, and 5 d after pollination (DAP) and endosperms at 7, 10, and 15 DAP, using B73 byMo17reciprocal crosses.Weobserved gradually increased expression of paternal transcripts in 3- and 5-DAP kernels. In 7-DAP endosperm, the majority of the genes tested reached a 2:1 maternal versus paternal ratio, suggesting that paternal genes are nearly fully activated by 7 DAP. …

Real-Time Quantitative Pcr Assays For Evaluation Of Soybean Varieties For Resistance To The Stem And Root Rot Pathogen Phytophthora Sojae, Mursel Catal, Fedai Erler, Dennis W. Fullbright, Gerard C. Adams

Department of Plant Pathology: Faculty Publications

Phytophthora root and stem rot caused by Phytophthora sojae is one of the most destructive disease of soybeans in the world. Effective management of the disease depends on selection and use of soybean varieties resistant to the disease. Fast and reliable procedures are vital to screen soybean varieties against the pathogen. Novel real-time quantitative (qPCR) assays were developed for both absolute and relative quantification of P. sojae in infected root tissues. QPCR assays were based on the detection of the internal transcribed spacer (ITS) gene of the pathogen and 18S ribosomal gene of the host plant. Absolute qPCR allowed the …

Abiotic And Biotic Factors Affecting The Japanese Beetle In Arkansas, Bryan Mathew Petty

Graduate Theses and Dissertations

Japanese beetles are a relatively new pest to Arkansas. During my Ph.D. research I investigated the pathogens and environmental factors influencing Japanese beetle populations in the state. The prevalence of various pathogens and parasitoids attacking Popillia japonica were recorded annually from wild populations. Of specific interest was the microsporidian pathogen Ovavesicula popilliae, which I introduced as a biological control agent in the state. Details of the relationship between this pathogen and the Japanese beetle were investigated, including dose response, host range, and spore production. Additionally, annual abundance of the beetle in the region was recorded and tracked over the course …

Identification Of Species Of Botryosphaeriaceae Causing Bot Gummosis In Citrus In California, A.O. Adesemoye, J.S. Mayorquin, D.H. Wang, M. Twizeyimana, S.C. Lynch, Akif Eskalen

Department of Plant Pathology: Faculty Publications

Members of the Botryosphaeriaceae family are known to cause Bot gummosis on many woody plants worldwide. To identify pathogens associated with Bot gummosis on citrus in California, scion and rootstock samples were collected in 2010 and 2011 from five citrusgrowing counties in California. Symptoms observed on citrus included branch cankers, dieback, and gumming. Various fungal species were recovered from necrotic tissues of branch canker and rootstock samples. Species were identified morphologically and by phylogenetic comparison as ‘Eureka’ lemon, ‘Valencia’, ‘Washington Navel’, ‘Fukumoto’, grapefruit, ‘Satsuma’, and ‘Meyer’ lemon. Species were identified morphologically and by phylogenetic comparison of the complete sequence of …

Plant Micrornas Display Differential 3' Truncation And Tailing Modifications That Are Argonaute1 Dependent And Conserved Across Species, Jixian Zhai, Yuanyuan Zhao, Stacey A. Simon, Sheng Huang, Katherine Petsch, Siwaret Arikit, Manoj Pillay, Lijuan Ji, Meng Xie, Xiaofeng Cao, Bin Yu, Marja Timmermans, Bing Yang, Xuemei Chen, Blake C. Meyers

Center for Plant Science Innovation: Faculty Publications

Plant small RNAs are 3' methylated by the methyltransferase HUA1 ENHANCER1 (HEN1). In plant hen1 mutants, 3' modifications of small RNAs, including oligo-uridylation (tailing), are associated with accelerated degradation of microRNAs (miRNAs). By sequencing small RNAs of the wild type and hen1 mutants from Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays), we found 39 truncation prior to tailing is widespread in these mutants. Moreover, the patterns of miRNA truncation and tailing differ substantially among miRNA families but are conserved across species. The same patterns are also observable in wild-type libraries from a broad …

Genetic Diversity Of Seed Dormancy And Molecular Evolution Of Weedy Red Rice, Te Ming Tseng

Graduate Theses and Dissertations

Rice is the grain with the third-highest global production. In the US, Arkansas is the largest rice producing state; however, an estimated 62% of the rice fields in the state are infested with red rice, and can cause up to 80% yield reduction in rice. Among its weedy traits, seed dormancy plays an important role in its persistence, and helps red rice escape weed management techniques thereby increasing the red rice soil seedbank. Red rice also has the potential to hybridize among themselves and with cultivated rice, thus resulting in diverse phenotypes and genotypes. In this study we measured variation …

Uromyces Appendiculatus In Honduras: Pathogen Diversity And Host Resistance Screening, Maricelis Acevedo, James R. Steadman, Juan C. Rosas

Department of Plant Pathology: Faculty Publications

Bean rust, caused by the fungus Uromyces appendiculatus, is a major constraint for common bean production worldwide. Virulence of U. appendiculatus collected from wild and cultivated Phaseolus spp. was examined in 28 locations across Honduras. Host accessions representing wild and domesticated Phaseolus spp. collected at the same sampling locations were evaluated for resistance against U. appendiculatus. In total, 91 pathotypes were identified from 385 U. appendiculatus isolates according to their virulence on each of the 12 host differentials. No significant difference in pathogen total virulence, measured as the mean disease score, was found between locations. However, significant differences …

Citrus Tristeza Virus-Host Interactions, W. O. Dawson, S. M. Garnsey, Satyanarayana Tatineni, S. Y. Folimonova, S. J. Harper, S. Gowda

Department of Plant Pathology: Faculty Publications

Citrus tristeza virus (CTV) is a phloem-limited virus whose natural host range is restricted to citrus and related species. Although the virus has killed millions of trees, almost destroying whole industries, and continually limits production in many citrus growing areas, most isolates are mild or symptomless in most of their host range. There is little understanding of how the virus causes severe disease in some citrus and none in others. Movement and distribution of CTV differs considerably from that of well-studied viruses of herbaceous plants where movement occurs largely through adjacent cells. In contrast, CTV systemically infects plants mainly by …

Neofusicoccum Luteum As A Pathogen On Tejocote (Crataegus Mexicana), Anthony O. Adesemoye, Joey S. Mayorquin, Akif Eskalen

Department of Plant Pathology: Faculty Publications

Tejocote (Crataegus mexicana), a small pome crab-apple-like fruit, is becoming economically important in California with increasing production, so consideration of diseases that hinder the yield is important. Diseased trees of tejocote were observed in four orchards of Riverside and San Diego Counties of California. Ten symptomatic/asymptomatic samples were studied from each of the orchards. Five most frequently isolated fungi were identified on the basis of morphological characters and sequence data of the internal transcribed spacer ITS1-5.8SITS2 and partial β-tubulin gene. Three isolates were identified as Neofusicoccum luteum and two as Phomopsis sp. Pathogenicity tests were conducted by inoculating …

Pseudomonas Hopu1 Modulates Plant Immune Receptor Levels By Blocking The Interaction Of Their Mrnas With Grp7, Valerie Nicaise, Anna Joe, Byeong-Ryool Jeong, Christin Korneli, Freddy Boutrot, Isa Westedt, Dorothee Staiger, James R. Alfano, Cyril Zipfel

Center for Plant Science Innovation: Faculty Publications

Pathogens target important components of host immunity to cause disease. The Pseudomonas syringae type III-secreted effector HopU1 is a mono-ADP-ribosyltransferase required for full virulence on Arabidopsis thaliana. HopU1 targets several RNA-binding proteins including GRP7, whose role in immunity is still unclear. Here, we show that GRP7 associates with translational components, as well as with the pattern recognition receptors FLS2 and EFR. Moreover, GRP7 binds specifically FLS2 and EFR transcripts in vivo through its RNA recognition motif. HopU1 does not affect the protein–protein associations between GRP7, FLS2 and translational components. Instead, HopU1 blocks the interaction between GRP7 and FLS2 and …

Small Interfering Rna–Mediated Translation Repression Alters Ribosome Sensitivity To Inhibition By Cycloheximide In Chlamydomonas Reinhardtii, Xinrong Ma, Eun-Jeong Kim, Insun Kook, Fangrui Ma, Adam Voshall, Etsuko N. Moriyama, Heriberto D. Cerutti

Center for Plant Science Innovation: Faculty Publications

Small RNAs (sRNAs; approximately 20 to 30 nucleotides in length) play important roles in gene regulation as well as in defense responses against transposons and viruses in eukaryotes. Their biogenesis and modes of action have attracted great attention in recent years. However, many aspects of sRNA function, such as the mechanism(s) of translation repression at postinitiation steps, remain poorly characterized. In the unicellular green alga Chlamydomonas reinhardtii, sRNAs derived from genomeintegrated inverted repeat transgenes, perfectly complementary to the 39 untranslated region of a target transcript, can inhibit protein synthesis without or with only minimal mRNA destabilization. Here, we report …

Strong Genetic Differentiation Between North American And European Populations Of Phytophthora Alni Subsp. Uniformis, Jaime Aguayo, Gerard C. Adams, Fabien Halkett, Mursel Catal, Claude Husson, Zoltán Á. Nagy, Everett M. Hansen, Benoît Marçais, Pascal Frey

Department of Plant Pathology: Faculty Publications

Alder decline caused by Phytophthora alni has been one of the most important diseases of natural ecosystems in Europe during the last 20 years. The emergence of P. alni subsp. alni—the pathogen responsible for the epidemic—is linked to an interspecific hybridization event between two parental species: P. alni subsp. multiformis and P. alni subsp. uniformis. One of the parental species, P. alni subsp. uniformis, has been isolated in several European countries and, recently, in North America. The objective of this work was to assess the level of genetic diversity, the population genetic structure, and the putative reproduction …

Isolation And Characterization Of The Grain Mold Fungi Cochliobolus And Alternaria Spp. From Sorghum Using Semiselective Media And Dna Sequence Analyses, Deanna L. Funnell-Harris, Louis K. Prom, Jeffrey F. Pedersen

Department of Plant Pathology: Faculty Publications

Mold diseases, caused by fungal complexes including Alternaria, Cochliobolus, and Fusarium species, limit sorghum grain production. Media were tested by plating Fusarium thapsinum, Alternaria sp., and Curvularia lunata, individually and competitively. Dichloran chloramphenicol rose bengal (DRBC) and modified V8 juice (ModV8) agars, found to be useful, were compared with commonly used agar media, dichloran chloramphenicol peptone (DCPA) and pentachloronitrobenzene (PCNB). Radial growth, starting with mycelia or single-conidia and hyphal tips, demonstrated an effect of media. For isolation of grain fungi, DRBC and ModV8 were similar or superior to DCPA and PCNB. When seedlings were inoculated with conidia of C. lunata, …

Occurrence And Distribution Of Triticum Mosaic Virus In The Central Great Plains, E. Byamukama, D. L. Seifers, G. L. Hein, E. De Wolf, N. A. Tisserat, M. A. C. Langham, L. E. Osborne, A. Timmerman, S. N. Wegulo

Department of Plant Pathology: Faculty Publications

Wheat curl mite (WCM)-transmitted viruses—namely, Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and the High Plains virus (HPV)—are three of the wheat-infecting viruses in the central Great Plains of the United States. TriMV is newly discovered and its prevalence and incidence are largely unknown. Field surveys were carried out in Colorado, Kansas, Nebraska, and South Dakota in spring and fall 2010 and 2011 to determine TriMV prevalence and incidence and the frequency of TriMV co-infection with WSMV or HPV in winter wheat. WSMV was the most prevalent and was detected in 83% of 185 season–counties (= s-counties), 73% …

Product Comparison Of Foliar Fungicide Efficacy On Diseases Of Field Corn In Nebraska, 2013, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Corn hybrid NK ‘N68B’, rating of “fair” (7 out of 9) for gray leaf spot (GLS), not rated for common rust (CR), and “excellent” (2 out of 9) for southern rust (SR), was planted on 15 May in 30-in. rows at a target population of 31,763 plants/A. The trial area was disked with corn as the previous year’s crop. Eight treatments and a non-treated control were replicated six times in a randomized complete block design. Each plot was four rows …

Complementarity To An Mirna Seed Region Is Sufficient To Induce Moderate Repression Of A Target Transcript In The Unicellular Green Alga Chlamydomonas Reinhardtii, Tomohito Yamasaki, Adam Voshall, Eun-Jeong Kim, Etsuko N. Moriyama, Heriberto Cerutti, Takeshi Ohama

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are 20–24 nt noncoding RNAs that play important regulatory roles in a broad range of eukaryotes by pairing with mRNAs to direct post-transcriptional repression. The mechanistic details of miRNA-mediated post-transcriptional regulation have been well documented in multicellular model organisms. However, this process remains poorly studied in algae such as Chlamydomonas reinhardtii, and specific features of miRNA biogenesis, target mRNA recognition and subsequent silencing are not well understood. In this study, we report on the characterization of a Chlamydomonas miRNA, cre-miR1174.2, , which is processed from a near-perfect hairpin RNA. Using Gaussia luciferase (gluc) reporter genes, …

Camelina Seed Transcriptome: A Tool For Meal And Oil Improvement And Translational Research, Huu T. Nguyen, Jillian E. Silva, Ram Podicheti, Jason Macrander, Wenyu Yang, Tara J. Nazarenus, Jeong-Won Nam, Jan G. Jaworski, Chaofu Lu, Brian E. Scheffler, Keithanne Mockaitis, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Camelina (Camelina sativa), a Brassicaceae oilseed, has received recent interest as a biofuel crop and production platform for industrial oils. Limiting wider production of camelina for these uses is the need to improve the quality and content of the seed protein-rich meal and oil, which is enriched in oxidatively unstable polyunsaturated fatty acids that are deleterious for biodiesel. To identify candidate genes for meal and oil quality improvement, a transcriptome reference was built from 2047 Sanger ESTs and more than 2 million 454-derived sequence reads, representing genes expressed in developing camelina seeds. The transcriptome of approximately 60K transcripts …

Comparative Analyses Of Two Geraniaceae Transcriptomes Using Next-Generation Sequencing, Jinxin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen

Center for Plant Science Innovation: Faculty Publications

Background: Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum.

Results: Normalized cDNA libraries of G. maderense and …

Arabidopsis 56–Amino Acid Serine Palmitoyltransferase- Interacting Proteins Stimulate Sphingolipid Synthesis, Are Essential, And Affect Mycotoxin Sensitivity, Athen N. Kimberlin, Saurav Majumder, Gongshe Han, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Teresa M. Dunn, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Maintenance of sphingolipid homeostasis is critical for cell growth and programmed cell death (PCD). Serine palmitoyltransferase (SPT), composed of LCB₁ and LCB₂ subunits, catalyzes the primary regulatory point for sphingolipid synthesis. Small subunits of SPT (ssSPT) that strongly stimulate SPT activity have been identified in mammals, but the role of ssSPT in eukaryotic cells is unclear. Candidate Arabidopsis thaliana ssSPTs, ssSPTa and ssSPTb, were identified and characterized. Expression of these 56–amino acid polypeptides in a Saccharomyces cerevisiae SPT null mutant stimulated SPT activity from the Arabidopsis LCB₁/LCB₂ heterodimer by >100-fold through physical interaction with LCB …

Pseudomonas Syringae Pv. Syringae Uses Proteasome Inhibitor Syringolin A To Colonize From Wound Infection Sites, Johana C. Misas-Villamil, Izabella Kolodziejek, Emerson Crabill, Farnusch Kaschani, Sherry Niessen, Takayuki Shindo, Markus Kaiser, James R. Alfano, Renier A. L. Van De Hoorn

Center for Plant Science Innovation: Faculty Publications

Infection of plants by bacterial leaf pathogens at wound sites is common in nature. Plants defend wound sites to prevent pathogen invasion, but several pathogens can overcome spatial restriction and enter leaf tissues. The molecular mechanisms used by pathogens to suppress containment at wound infection sites are poorly understood. Here, we studied Pseudomonas syringae strains causing brown spot on bean and blossom blight on pear. These strains exist as epiphytes that can cause disease upon wounding caused by hail, sand storms and frost. We demonstrate that these strains overcome spatial restriction at wound sites by producing syringolin A (SylA), a …

Functional Modeling Identifies Paralogous Solanesyl-Diphosphate Synthases That Assemble The Side Chain Of Plastoquinone-9 In Plastids, Anna Block, Rikard Fristedt, Sara Rogers, Jyothi Kumar, Brian Barnes, Joshua Barnes, Christian Elowsky, Yashitola Wamboldt, Sally Ann Mackenzie, Kevin Redding, Sabeeha S. Merchant, Gilles J. Basset

Center for Plant Science Innovation: Faculty Publications

Background: Plastid isoforms of solanesyl-diphosphate synthase catalyze the elongation of the prenyl side chain of plastoquinone-9.

Results: Corresponding mutants display lower levels of plastoquinone-9 and plastochromanol-8 and display intact levels of vitamin E.

Conclusion: Plastochromanol-8 originates from a subfraction of non-photoactive plastoquinol-9 and is not essential for seed longevity.

Significance: Viable plastoquinone-9 mutants are invaluable tools for understanding plastid metabolism.

Mutational Analyses Of A Fork Head Associated Domain Protein, Dawdle, In Arabidopsis Thaliana, Lakshmi Ayiloor Narayanan, Dipaloke Mukherjee, Shuxin Zhang, Bin Yu, David Chevalier

Center for Plant Science Innovation: Faculty Publications

DAWDLE (DDL) gene encodes a protein that contains an N-terminal arginine-rich domain and a C-terminal Fork Head Associated (FHA) domain in Arabidopsis thaliana. DDL protein is believed to function in microRNA biogenesis by mediating the recruitment of pri-microRNA to DICER-LIKE 1 and also stabilizing the microRNA. The aim of this study was to conduct a structure-function analysis to identify the regions in DDL that are of functional significance. Targeted Induced Local Lesions in Genome screen was performed in the Columbia erecta-105 background of Arabidopsis resulting in the identification of eight point mutations spanning DDL. The mutants were characterized by …

Cdc5, A Dna Binding Protein, Positively Regulates Posttranscriptional Processing And/Or Transcription Of Primary Microrna Transcripts, Shuxin Zhang, Meng Xie, Guodong Ren, Bin Yu

Center for Plant Science Innovation: Faculty Publications

CDC5 is a MYB-related protein that exists in plants, animals, and fungi. In Arabidopsis, CDC5 regulates both growth and immunity through unknown mechanisms. Here, we show that CDC5 from Arabidopsis positively regulates the accumulation of microRNAs (miRNAs), which control many biological processes including development and adaptations to environments in plants. CDC5 interacts with both the promoters of genes encoding miRNAs (MIR) and the DNA-dependent RNA polymerase II. As a consequence, lack of CDC5 reduces the occupancy of polymerase II at MIR promoters, as well as MIR promoter activities. In addition, CDC5 is associated with the DICER–LIKE1 complex, …

Comparative Studies Of Differential Gene Calling Using Rna-Seq Data, Ximeng Zheng, Etsuko N. Moriyama

Center for Plant Science Innovation: Faculty Publications

Background: With its massive amount of data, gene-expression profiling by RNA-Seq has many advantanges compared with microarray experiments. RNA-Seq analysis, however, is fundamentally different from microarray data analysis. Techniques developed for analyzing microarray data thus cannot be directly applicable for the digital gene expression data. Several statistical methods have been developed for identifying differentially expressed genes specifically from RNA-Seq data over the past few years.
Results: In this study, we examined the performance of differential gene-calling methods using RNA-Seq data in practical situations. We focused on two representative methods: one parametric method, DESeq, and one nonparametric method, NOISeq. …

A Novel Function Prediction Approach Using Protein Overlap Networks, Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Construction of a reliable network remains the bottleneck for network-based protein function prediction. We built an artificial network model called protein overlap network (PON) for the entire genome of yeast, fly, worm, and human, respectively. Each node of the network represents a protein, and two proteins are connected if they share a domain according to InterPro database.
Results: The function of a protein can be predicted by counting the occurrence frequency of GO (gene ontology) terms associated with domains of direct neighbors. The average success rate and coverage were 34.3% and 43.9%, respectively, for the test genomes, …

A Thraustochytrid Diacylglycerol Acyltransferase 2 With Broad Substrate Specificity Strongly Increases Oleic Acid Content In Engineered Arabidopsis Thaliana Seeds, Chunyu Zhang, Umidjon Iskandarov, Elliott T. Klotz, Robyn L. Stevens, Rebecca E. Cahoon, Tara J. Nazarenus, Suzette L. Pereira, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Diacylglycerol acyltransferase (DGAT) catalyses the last step in acyl-CoA-dependent triacylglycerol (TAG) biosynthesis and is an important determinant of cellular oil content and quality. In this study, a gene, designated TaDGAT2, encoding a type 2 DGAT (DGAT2)-related enzyme was identified from the oleaginous marine protist Thraustochytrium aureum. The deduced TaDGAT2 sequence contains a ~460 amino acid domain most closely related to DGAT2s from Dictyostelium sp. (45–50% identity). Recombinant TaDGAT2 restored TAG biosynthesis to the Saccharomyces cerevisiae H1246 TAG-deficient mutant, and microsomes from the complemented mutant displayed DGAT activity with C16 and C18 saturated and unsaturated fatty acyl-CoA and diacylglycerol …