Life Sciences Commons^™

Translational Genomics For Alfalfa Varietal Improvement, G. D. May

IGC Proceedings (1997-2023)

Key points

1. Medicago truncatula is a model legume with available mapping, genome, and RNA, protein and metabolite profiling databases and genetically diverse populations.
2. Genomics resources developed for M. truncatula have application in the study and improvement of alfalfa making it an excellent model for this forage legume.

Nuclear Phylogeny And Insights Into Whole-Genome Duplications And Reproductive Development Of Solanaceae Plants, Jie Wang, Weibin Xu, Junwen Zhai, Yi Hu, Jing Guo, Caifei Zhang, Yiyong Zhao, Lin Zhang, Christopher T. Martine, Hong Ma, Chien-Hsun Huang

Faculty Journal Articles

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, …

Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

BACKGROUND: The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.

RESULTS: We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms …

Complete Genome Sequence Of The Pantoea Phage Ah07, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages of the phyllosphere have not been extensively described, despite their role in bacterial communities on this plant organ. Here, we describe a temperate Pantoea phage, AH07, that was isolated from the leaves of horse chestnut trees. The 37,859-bp linear double-stranded DNA genome contains 58 putative genes, including an integration cassette.

Complete Genome Sequences Of Four Phages Of The Horse Chestnut Phyllosphere, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages play important roles in determining bacterial communities, including plant microbiota. Here, we describe four lytic phages, three Siphoviridae and one Podoviridae, isolated from four different bacterial species found on the leaves of horse chestnut trees. Their double-stranded DNA (dsDNA) genomes range from 39,095 to 46,062 bp and contain 51 to 70 genes.

Using Multi-Omics Approaches To Study Flowering Time And Fruit Development In Perennial Fruit Species, Jiali Yu

Doctoral Dissertations

Perennial fruiting plants coordinate their reproductive activities with seasonal changes in the temperate climates, with a pattern of bud set, dormancy establishment, fulfillment of chilling, flowering, fruit set, and fruit ripening. These processes have been optimized for the production of orchard plants that reliably produce quality fruit for human consumption. The understanding of molecular controls of dormancy in fruit trees has grown rapidly in the past decade, however, the complex mechanisms remain largely unknown. This dissertation presents my findings on genetic and epigenetic changes in Prunus species from dormancy to flowering using transcriptomics and epigenomics approaches. First, I compared the …

Comprehensive Analysis Of Nac Transcription Factor Family Uncovers Drought And Salinity Stress Response In Pearl Millet (Pennisetum Glaucum), Ambika Dudhate, Harshraj Shinde, Pei Yu, Daisuke Tsugama, Shashi Kumar Gupta, Shenkui Liu, Tetsuo Takano

Pharmaceutical Sciences Faculty Publications

BACKGROUND: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet.

RESULTS: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight …

Allelic Share Among Two Taxonomically Related Elymus Species, Hexaploidy E. Nutans Griseb And Tetraploid E. Burchan‐Buddae (Nevski) Tzvelev, Xuebing Yan, Chengzhang Wang, Yuxia Guo, Yibao Jiang, Defeng Li

IGC Proceedings (1997-2023)

No abstract provided.

Genetic Characterization And Genome-Wide Association Mapping For Dwarf Bunt Resistance In Bread Wheat Accessions From The Usda National Small Grains Collection, Tyler Gordon, Rui Wang, David Hole, Harold Bockelman, J. Michael Bonman, Jianli Chen

Plants, Soils, and Climate Faculty Publications

Key message

Dwarf bunt-resistant bread wheat accessions and SNP markers associated with DB resistance identified in this study are valuable resources for characterization and deployment of DB resistance in bread wheat.

Abstract

Dwarf bunt (DB), caused by Tilletia controversa J.G. Kühn, can significantly reduce grain yield and quality on autumn-sown wheat in regions with prolonged snow cover. DB can be managed with the use of resistant cultivars. The objectives of the present study were to characterize DB resistance in a large set of bread wheat accessions from the National Small Grains Collection and use a genome-wide association study approach to …

Diversity And Cross-Infection Potential Of Colletotrichum On Apples And Small Fruits In Kentucky Mixed-Fruit Orchards, Madison Julia Eaton

Theses and Dissertations--Plant Pathology

Fungi in the genus Colletotrichum cause apple, blueberry, and strawberry fruit rots, which result in significant losses for Kentucky growers. Most orchards in Kentucky are agritourism-focused and grow multiple fruits in close proximity. These mixed-fruit orchards may facilitate Colletotrichum cross-infection, which has serious management implications. Small fruit and apple Colletotrichum isolates from Kentucky orchards were characterized by morphotype, phylogenetic species identification, cross-inoculation, genome sequencing, and telomere fingerprinting. The small fruit isolates grouped into seven morphotypes, representing two species complexes: C. acutatum and C. gloeosporioides. All blueberry isolates belonged to the species C. fioriniae, and the majority of strawberry …

Evolutionary Genomics Of Dynamic Sex Chromosomes In The Salicaceae, Ran Zhou

Graduate Theses, Dissertations, and Problem Reports

Identifying the sex-determination region (SDR) and other genomic features of sex chromosomes are of great importance in the studies of the evolution of sex. However, the process of accurately identifying the size and location of the SDR is often difficult, even when a genomic sequence is available. This usually is hindered by large repetitive elements and a lack of recombination in the SDR. In this thesis, I assemble sex chromosomes with whole genomic sequencing data, identify SDRs and explore their genomic features in two sister species from the Salicaceae family. I also develop an interpretation of the lability of the …

Molecular And Morphological Variation Among Populations Of Pediomelum Tenuiflorum (Pursh) A.N. Egan (Fabaceae) In Nebraska, Usa, Chauncey L. Kellar Jr., Roxi Kellar

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Individuals of Pediomelum tenuiflorum, “wild alfalfa”, from disjunct populations in Nebraska vary extensively in their overall gestalt. Those in the western and central part of the state have a very slender growth habit, with thin stems and few, small flowers; whereas, those in the southeast have a very robust growth habit with heavy-looking stems and many tightly clustered flowers. For nearly 200 years, taxonomists have alternated between splitting P. tenuiflorum into two species, with the many-flowered morphotype named P. floribundum, and lumping all the morphological variants into one species as they are now. In this study, we investigated …

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Biology Faculty Publications

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of …

Genotyping By Sequencing And Genome–Environment Associations In Wild Common Bean Predict Widespread Divergent Adaptation To Drought, Andrés J. Cortés, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations (GEA) in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using genotyping by sequencing (GBS) to discover single nucleotide polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a …

Maize Genomes To Fields: 2014 And 2015 Field Season Genotype, Phenotype, Environment, And Inbred Ear Image Datasets, Naser Alkhalifah, Darwin A. Campbell, Celeste M. Falcon, Jack M. Gardiner, Nathan D. Miller, Maria Cinta Romay, Ramona Walls, Renee Walton, Cheng-Ting Yeh, Martin Bohn, Jessica Bubert, Edward S. Buckler, Ignacio Ciampitti, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice Hirsch, James B. Holland, David Hooker, Shawn Kaeppler, Joseph Knoll, Nick Lauter, Elizabeth C. Lee, Aaron Lorenz, Jonathan P. Lynch, Stephen P. Moose, Seth C. Murray, Rebecca Nelson, Torbert Rocheford, Oscar Rodriguez, James C. Schnable, Brian Scully, Margaret Smith, Nathan Springer, Peter Thomison, Mitchell Tuinstra, Randall J. Wisser, Wenwei Xu, David Ertl, Patrick S. Schnable, Natalia De Leon, Edgar P. Spalding, Jode Edwards, Carolyn J. Lawrence-Dill

Department of Agronomy and Horticulture: Faculty Publications

Objectives: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F’s genotype by environment project has released 2014 and 2015 datasets to the public, with …

Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook

Center for Plant Science Innovation: Faculty and Staff Publications

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, …

Genetic Analysis Of Field Populations Of The Plant Pathogens Cercospora Sojina, Corynespora Cassiicola And Phytophthora Colocasiae, Sandesh Kumar Shrestha

Doctoral Dissertations

Genetic markers and whole genome sequencing (WGS) were used to study the disease dynamics and population structure for three important plant pathogens; Cercospora sojina (frogeye leaf spot of soybean), Corynespora cassiicola (target spot of soybean, cotton and many other crops) and Phytophthora colocasiae (taro leaf blight). For each pathogen, genome sequencing was used to guide the development of single nucleotide polymorphism (SNP) markers and both were used to investigate diversity in field populations. Investigation of C. sojina in Tennessee included comparisons of extant populations and historical isolates, revealing a dominant, potentially long-lived, clonal lineage. Characterization of QoI fungicide resistance indicates …

Phages Of Non-Diary Lactococci: Isolation And Characterization Of Phi L47, A Phage Infecting The Grass Isolate Lactococcus Lactis Ssp Cremoris Dpc6860, Daniel Cavanagh, Caitríona M. Guinane, Horst Neve, Aidan Coffey, R. Paul Ross, Gerald F. Fitzgerald, Olivia Mcauliffe

Department of Biological Sciences Publications

Lactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron …

Myb10 And Myb72 Are Required For Growth Under Iron-Limiting Conditions, Christine M. Palmer, Maria N. Hindt, Holger Schmidt, Stephan Clemens, Mary Lou Guerinot

Dartmouth Scholarship

Iron is essential for photosynthesis and is often a limiting nutrient for plant productivity. Plants respond to conditions of iron deficiency by increasing transcript abundance of key genes involved in iron homeostasis, but only a few regulators of these genes have been identified. Using genome-wide expression analysis, we searched for transcription factors that are induced within 24 hours after transferring plants to iron-deficient growth conditions. Out of nearly 100 transcription factors shown to be up-regulated, we identified MYB10 and MYB72 as the most highly induced transcription factors. Here, we show that MYB10 and MYB72 are functionally redundant and are required …

Phycodnaviruses: A Peek At Genetic Diversity, David Dunigan, Lisa Fitzgerald, James L. Van Etten

David D Dunigan Ph. D.

The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The …

Evolutionary Genomics Of Mycovirus-Related Dsrna Viruses Reveals Cross-Family Horizontal Gene Transfer And Evolution Of Diverse Viral Lineages, Huiquan Liu, Yanping Fu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Youliang Peng, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

BACKGROUND: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses.

RESULTS: In this study, we report the molecular properties of two novel dsRNA mycoviruses that …

Development And Functional Analysis Of Novel Genetic Promoters Using Dna Shuffling, Hybridization And A Combination Thereof, Rajiv Ranjan, Sunita Patro, Bhubaneswar Pradhan, Alok Kumar, Indu B. Maiti, Nrisingha Dey

Kentucky Tobacco Research and Development Center Faculty Publications

BACKGROUND: Development of novel synthetic promoters with enhanced regulatory activity is of great value for a diverse range of plant biotechnology applications.

METHODOLOGY: Using the Figwort mosaic virus full-length transcript promoter (F) and the sub-genomic transcript promoter (FS) sequences, we generated two single shuffled promoter libraries (LssF and LssFS), two multiple shuffled promoter libraries (LmsFS-F and LmsF-FS), two hybrid promoters (FuasFScp and FSuasFcp) and two hybrid-shuffled promoter libraries (LhsFuasFScp and LhsFSuasFcp). Transient expression activities of approximately 50 shuffled promoter clones from each of these libraries were assayed in tobacco (Nicotiana tabacum cv. Xanthi) protoplasts. It was observed that most …

Adventures In The Enormous: A 1.8 Million Clone Bac Library For The 21.7 Gb Genome Of Loblolly Pine., Zenaida V. Magbanua, Seval Ozkan, Benjamin D. Bartlett, Philippe Chouvarine, Christopher A. Saski, Aaron Liston, Richard C. Cronn, C. Dana Nelson, Daniel G. Peterson

College of Agriculture & Life Sciences Publications and Scholarship

Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb …

Abundant Degenerate Miniature Inverted-Repeat Transposable Elements In Genomes Of Epichloid Fungal Endophytes Of Grasses, Damien J Fleetwood, Anar K Khan, Richard D Johnson, Carolyn A Young, Shipra Mittal, Ruth E Wrenn, Uljana Hesse, Simon J Foster, Christopher L. Schardl, Barry Scott

Plant Pathology Faculty Publications

Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration …

Genomic Perspectives On Evolution In Bracken Fern, Joshua P. Der

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global …

Distinct Evolutionary Histories Of The Dna-A And Dna-B Components Of Bipartite Begomoviruses, Rob W. Briddon, Basavaprabhu L. Patil, Basavaraj Bagewadi, Muhammad Shah Nawaz-Ul-Rehman, Claude M. Fauquet

Plant Pathology Faculty Publications

BACKGROUND: Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a …

Copy Number Variation Shapes Genome Diversity In Arabidopsis Over Immediate Family Generational Scales, Seth Debolt

Horticulture Faculty Publications

Arabidopsis thaliana is the model plant and is grown worldwide by plant biologists seeking to dissect the molecular underpinning of plant growth and development. Gene copy number variation (CNV) is a common form of genome natural diversity that is currently poorly studied in plants and may have broad implications for model organism research, evolutionary biology, and crop science. Herein, comparative genomic hybridization (CGH) was used to identify and interrogate regions of gene CNV across the A. thaliana genome. A common temperature condition used for growth of A. thaliana in our laboratory and many around the globe is 22 degrees C. …

The Genome Of Nectria Haematococca: Contribution Of Supernumerary Chromosomes To Gene Expansion, Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-Jun Ma, Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, Hans D. Vanetten

Plant Pathology Faculty Publications

The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 …

Evolution Of A Subtilisin-Like Protease Gene Family In The Grass Endophytic Fungus Epichloë Festucae, Michelle K. Bryant, Christopher L. Schardl, Uljana Hesse, Barry Scott

Plant Pathology Faculty Publications

BACKGROUND: Subtilisin-like proteases (SLPs) form a superfamily of enzymes that act to degrade protein substrates. In fungi, SLPs can play either a general nutritive role, or may play specific roles in cell metabolism, or as pathogenicity or virulence factors.

RESULTS: Fifteen different genes encoding SLPs were identified in the genome of the grass endophytic fungus Epichloë festucae. Phylogenetic analysis indicated that these SLPs belong to four different subtilisin families: proteinase K, kexin, pyrolysin and subtilisin. The pattern of intron loss and gain is consistent with this phylogeny. E. festucae is exceptional in that it contains two kexin-like genes. Phylogenetic analysis …

A Discontinuous Rna Platform Mediates Rna Virus Replication: Building An Integrated Model For Rna-Based Regulation Of Viral Processes, Baodong Wu, Judit Pogany, Hong Na, Beth L. Nicholson, Peter D. Nagy, K. Andrew White

Plant Pathology Faculty Publications

Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo …