Genetics and Genomics Commons^™

Draft Genome Sequence Of Cercospora Sojina Isolate S9, A Fungus Causing Frogeye Leaf Spot (Fls) Disease Of Soybean, Fanchang Zeng, Chaofan Wang, Guirong Zhang, Junmei Wei, Carl A. Bradley, Ray Ming

Plant Pathology Faculty Publications

Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. The fungus Cercospora sojina is a plant pathogen that threatens global soybean supplies. Here, we report the genome sequence of C. sojina strain S9 and detect genome features and predicted genomic elements. The genome sequence of C. sojina is a valuable resource with potential in studying the fungal pathogenicity and soybean host resistance to frogeye leaf spot (FLS), which is caused by C. sojina. …

Development Of Near-Isogenic Lines In A Parthenogenetically Reproduced Thrips Species, Frankliniella Occidentalis, Guangdi Yuan, Yanran Wan, Xiaoyu Li, Bingqing He, Youjun Zhang, Baoyun Xu, Shaoli Wang, Wen Xie, Xuguo Zhou, Qingjun Wu

Entomology Faculty Publications

Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study …

The Lx Report Of The Bean Improvement Cooperative No. 60, March 2017.

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

CONTENTS

LX Annual Report of the Bean Improvement Cooperative xi

BIC Coordinating Committee Membership - 1957 to 2017 . xii

BIC Meritorious Service and Distinguished Achievement Award Recipients - 1957 to 2015 xiii

BIC Awards Nomination Request for 2017 xvi

BIC/NAPIA Meeting in 2017 . xix

In Memory of Guillermo E. Galvez-Enriquez xx

RESEARCH PAPERS FOR 2017

OPTIMIZING SPORULATION OF Pseudocercospora griseola IN VITRO • Paula F. de Pádua1, Rafael Pereira1, Luanna B. W. Gomes1 and Elaine A. de Souza1* 1

FINE MAPPING THE BROAD SPECTRUM ANTHRACNOSE RESISTANCE GENE IN AMENDOIM CAVALO 3 • Gilio, T.A.S.1, Oscar P. Hurtado-Gonzales2, Giseli …

The Mirnaome Of Catharanthus Roseus: Identification, Expression Analysis, And Potential Roles Of Micrornas In Regulation Of Terpenoid Indole Alkaloid Biosynthesis, Ethan M. Shen, Sanjay Kumar Singh, Jayadri S. Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik

Plant and Soil Sciences Faculty Publications

MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus …

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.

Restoration Of The Iconic Pando Aspen Clone: Emerging Evidence Of Recovery, Paul C. Rogers, Jody A. Gale

Aspen Bibliography

Quaking aspen (Populus tremuloides Michx.) is being stressed across the America West from a variety of sources including drought, herbivory, fire suppression, development, and past management practices. Rich assemblages of plants and animals that utilize aspen forests, as well as economic values of tourism, grazing, hunting, and water conservation, make aspen ecosystems among the most valuable vegetation types in this region. The 43-ha Pando clone near Fish Lake, Utah, is an iconic example of an aspen community undergoing rapid decline due to overstory mortality and chronic recruitment failure. As part of a larger project to restore Pando, we fenced, …

A Comparative Genomic Analysis Of Putative Pathogenicity Genes In The Host-Specific Sibling Species Colletotrichum Graminicola And Colletotrichum Sublineola, Ester A. S. Buiate, Katia Viana Xavier, Neil Moore, Maria F. Torres, Mark L. Farman, Christopher L. Schardl, Lisa J. Vaillancourt

Plant Pathology Faculty Publications

Background: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.

Results: Inoculation of maize with C. sublineola …

The Family Rhabdoviridae: Mono- And Bipartite Negative-Sense Rna Viruses With Diverse Genome Organization And Common Evolutionary Origins, Ralf G. Dietzgen, Hideki Kondo, Michael M. Goodin, Gael Kurath, Nikos Vasilakis

Plant Pathology Faculty Publications

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- …

Structure Of The Chlorovirus Pbcv-1 Major Capsid Glycoprotein Determined By Combining Crystallographic And Carbohydrate Molecular Modeling Approaches, Cristina De Castro, Thomas Klose, Immacolata Speciale, Rosa Lanzetta, Antonio Molinaro, James L. Van Etten, Michael G. Rossmann

James Van Etten Publications

The glycans of the major capsid protein (Vp54) of Paramecium bursaria chlorella virus (PBCV-1) were recently described and found to be unusual. This prompted a reexamination of the previously reported Vp54 X-ray structure. A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling. The crystallographic data identified most of the monosaccharides located close to the protein backbone, but failed to detect those further from the glycosylation sites. Molecular modeling complemented this model by adding the missing monosaccharides and examined the conformational preference of the whole molecule, alone or within the crystallographic environment. Thus, combining …

Influence Of Mature Overstory Trees On Adjacent 12-Year Regeneration And The Woody Understory: Aggregated Retention Versus Intact Forest, Miranda T. Curzon, Susan C. Baker, Christel C. Kern, Brian J. Palik, Anthony W. D'Amato

Aspen Bibliography

No abstract provided.

Araucaria In The Urban Landscape: A Novel Leaning Pattern And Evidence Of Cultivated Hybridization, Jason W. Johns

Master's Theses

Our understanding of the natural world is constantly evolving and strengthening as more observations are made and experiments are performed. For example, we understand that tree stems grow toward the light (positive phototropism; Darwin 1880, Loehle 1986, Christie et al. 2013) and against gravity (negative gravitropism; Knight 1806, Hashiguchi et al. 2013). We also know that plants respond to mechanical stimulus and perturbation (thigmotropism; Braam 2005). Genes and their resulting proteins have been described to uncover some of the mechanisms for these environmental responses, but relatively speaking, we have just scratched the surface (Wyatt et al. 2013). While the discovery …

¬Multilocus Phylogeny Of The Lichen Family Megasporaceae, Tim B. Wheeler

Graduate Student Theses, Dissertations, & Professional Papers

The lichen symbiosis is one of the oldest studied mutualisms; in fact, Frank and De Bary coined the term "symbiosis" while studying lichens (Frank, 1877; De Bary 1879). The widespread, stable association between the mycobiont and photobiont in lichens offers an ideal system for the study of co-evolution. The recent application of molecular data to lichens has begun to unveil the complexities involved in these associations (Upreti et al. 2015, Spribille et al. 2016). Lichenized fungi make up a huge fraction of fungal diversity (Nash 2008), yet very little is known of their genetic diversity. Fungal taxonomy is notoriously difficult …

Conversion Of An Instantaneous Activating K+ Channel Into A Slow Activating Inward Rectifier, Dirk Baumeister, Brigitte Hertel, Indra Schroeder, Sabrina Gazzarrini, Stefan M. Kast, James L. Van Etten, Anna Moroni, Gerhard Thiel

James Van Etten Publications

The miniature channel, Kcv, is a structural equivalent of the pore of all K⁺ channels. Here, we follow up on a previous observation that a largely voltage-insensitive channel can be converted into a slow activating inward rectifier after extending the outer transmembrane domain by one Ala. This gain of rectification can be rationalized by dynamic salt bridges at the cytosolic entrance to the channel; opening is favored by voltage-sensitive formation of salt bridges and counteracted by their disruption. Such latent voltage sensitivity in the pore could be relevant for the understanding of voltage gating in complex Kv channels.

Structure Of The N-Glycans From The Chlorovirus Ne-Jv-1, Immacolata Speciale, Irina Agarkova, Garry Duncan, James L. Van Etten, Cristina De Castro

James Van Etten Publications

Results from recent studies are breaking the paradigm that all viruses depend on their host machinery to glycosylate their proteins. Chloroviruses encode several genes involved in glycan biosynthesis and some of their capsid proteins are decorated with N-linked oligosaccharides with unique features. Here we describe the elucidation of the N-glycan structure of an unusual chlorovirus, NE-JV-1, that belongs to the Pbi group. The host for NE-JV-1 is the zoochlorella Micractinium conductrix. Spectroscopic analyses established that this N-glycan consists of a core region that is conserved in all of the chloroviruses. The one difference is that the residue 3OMe-l-rhamnose is …

Improvement Of Milling And Nutritional Quality Characteristics Of Oats Through Genomic Selection, Sudha Neupane Adhikari

Electronic Theses and Dissertations

Oats can lower cholesterol, reduce risks of type-2 diabetes, and help prevent heart diseases when consumed daily. Therefore, it is important to evaluate and select breeding lines with desirable milling and nutritional quality traits. Genomic selection, which uses genotyping data to predict the breeding value of an individual, is a promising method to increase genetic gain by selecting for quality traits earlier in the line development process. In this study, we collected phenotypic data for three nutritional traits (protein, β- glucan, and fat content) and five milling quality traits (percent plumps, percent thins, percent plump groat, groat percent and thousand …

Guide To Quaking Aspen Ecology And Management With Emphasis On Bureau Of Land Management Lands In The Western United States, Paul C. Rogers

Aspen Bibliography

No abstract provided.

Genotypic Variability In Populus Tremula L. Affects How Anthropogenic Nitrogen Enrichment Influences Litter Decomposition, Franziska Bandau, Benedicte Riber Albrectsen, Riitta Julkunen-Tiitto, Michael J. Gundale

Aspen Bibliography

No abstract provided.

Can Carbon Fluxes Explain Differences In Soil Organic Carbon Storage Under Aspen And Conifer Forest Overstories?, Antra Boca, Helga Van Miegroet

Aspen Bibliography

No abstract provided.

Aspen Health On National Forests In The Northern Rocky Mountain Region, James T. Blodgett, Kurt K. Allen, Kendra Schotzko, Al Dymerski

Aspen Bibliography

No abstract provided.

Climatic Sensitivity Of A Mixed Forest Association Of White Spruce And Trembling Aspen At Their Southern Range Limit, Sophan Chhin, G. Geoff Wang

Aspen Bibliography

No abstract provided.

Post-Glacial Biogeography Of Trembling Aspen Inferred From Habitat Models And Genetic Variance In Quantitative Traits, Chen Ding, Stefan G. Schreiber, David R. Roberts, Andreas Hamann, Jean S. Brouard

Aspen Bibliography

No abstract provided.

Maintaining Ecosystem Resilience: Functional Responses Of Tree Cavity Nesters To Logging In Temperate Forests Of The Americas, Jose Tomas Ibarra, Michaela Martin, Kristina L. Cockle, Kathy Martin

Aspen Bibliography

Logging often reduces taxonomic diversity in forest communities, but little is known about how this biodiversity loss affects the resilience of ecosystem functions. We examined how partial logging and clearcutting of temperate forests influenced functional diversity of birds that nest in tree cavities. We used point-counts in a before-after-control-impact design to examine the effects of logging on the value, range, and density of functional traits in bird communities in Canada (21 species) and Chile (16 species). Clearcutting, but not partial logging, reduced diversity in both systems. The effect was much more pronounced in Chile, where logging operations removed critical nesting …

Quaking Aspen In The Northern Rockies Retention And Restoration, Camille Stevens-Rumann, Penelope Morgan, Eva Strand, Diane Abendroth

Aspen Bibliography

No abstract provided.

Assessment Of Aspen Ecosystem Vulnerability To Climate Change For The Uinta-Wasatch- Cache And Ashley National Forests, Utah, Janine Rice, Tim Bardsley, Pete Gomben, Dustin Bambrough, Stacey Weems, Allen Huber, Linda A. Joyce

Aspen Bibliography

No abstract provided.

Structural Studies Demonstrating A Bacteriophage-Like Replication Cycle Of The Eukaryote-Infecting Paramecium Bursaria Chlorella Virus-1, Elad Milrot, Eyal Shimoni, Katya Rechav, Tamar Unger, James L. Van Etten, Abraham Minsky

James Van Etten Publications

A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic- infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

Responding To Soil Fungal Communities: A Look At Interactions Between Arbuscular Mycorrhizal Fungi And The Common Yellow Monkeyflower, Mariah Mcintosh

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The obligate fungal mutualists arbuscular mycorrhizal fungi (AMF) colonize the roots approximately 80% of vascular plants, generally thought to provide mineral nutrition, pathogen protection, or drought resistance to plants in exchange for photosynthetic carbon. Because of the ecological and evolutionary significance of these interactions, much work has been done to understand this symbiosis at the community level. However, much remains to be understood about how AMF affect plant fitness on an individual level. In this study, we took advantage of the tractability of the emerging model species Mimulus guttatus, the common yellow monkeyflower, to identify genetic differences in how …

Uncovering Candidate Cold Tolerance Genes In Maize (Zea Mays), Raeann N. Goering

Departmental Honors Projects

With booming populations soon to overwhelm the world's food production capabilities, studying what makes crop organisms, like maize, efficient is crucial to ensure that the demand for food is met. Planting earlier in the spring would lengthen the crop season and produce larger yields provided the crop is tolerant to early spring’s low temperatures. Plants can adjust to abiotic stresses through biochemical changes controlled by transcription of genes. Trained plants can be produced by pre-exposing them to a lesser stress, allowing them to recover, then exposing them to a greater, longer stress. It is hypothesized that trained plants will tolerate …

Identification And Characterization Of Genes Involved In Metabolism Of N5 Monoene Precursors To N5 Anacardic Acids In The Trichomes Of Pelargonium X Hortorum., Richa A. Singhal

Electronic Theses and Dissertations

Unusual monoenoic fatty acids (UMFA’s) and specialized metabolites called anacardic acids (AnAc) are produced in glandular trichomes of Pelargonium ´ hortorum (geranium). The UMFA’s, 16:1^∆11 and 18:1^∆13 are precursors for the synthesis of unsaturated AnAc 22:1n5and 24:1n5 that contribute to pest resistance in geraniums. UMFAs and their derived AnAc metabolites not only provide a useful biological marker that differentiates the biosynthetic pathway for unusual mononenes from the common fatty acids (i.e. stearic, palmitic, oleic, linoleic and linolenic) but also have industrial, medical and agricultural applications. Fatty acid biosynthesis enzymes like acyl carrier proteins (ACPs); thioesterases (TEs) and β-ketoacyl-ACP …