Index Catalog // ScholarsArchive@OSU

A single generation of domestication heritably alters the expression of hundreds of genes

Creator:: Christie, Mark R., Marine, Melanie L., Fox, Samuel E., French, Rod A., and Blouin, Michael S.
Abstract:: The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis,...
Resource Type:: Article

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Creator:: Filichkin, Sergei A., Breton, Ghislain, Priest, Henry D., Dharmawardhana, Palitha, Jaiswal, Pankaj, Fox, Samuel E., Michael, Todd P., Chory, Joanne, Kay, Steve A., and Mockler, Todd C.
Abstract:: BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized...
Resource Type:: Article

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Creator:: Peremyslov, Valera V., Mockler, Todd C., Filichkin, Sergei A., Fox, Samuel E., Jaiswal, Pankaj, Makarova, Kira S., Koonin, Eugene V., and Dolja, Valerian V.
Abstract:: Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Resource Type:: Article

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Creator:: Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj
Abstract:: PREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. METHODS AND RESULTS: More than 350 million sequence reads from the mRNA libraries...
Resource Type:: Article

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

Creator:: Fox, Samuel E., Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K., Elser, Justin, Leonard, Jeffrey M., Sage, Abigail, Gresham, Cathy, Kerhornou, Arnaud, Bolser, Dan, McCarthy, Fiona, Kersey, Paul, Lazo, Gerard R., and Jaiswal, Pankaj
Abstract:: Background Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
Resource Type:: Article

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Creator:: Jeong, Dong-Hoon, Schmidt, Skye A., Rymarquis, Linda A., Park, Sunhee, Ganssmann, Matthias, German, Marcelo A., Accerbi, Monica, Zhai, Jixian, Fahlgren, Noah, Fox, Samuel E., Garvin, David F., Mockler, Todd C., Carrington, James C., Meyers, Blake C., and Green, Pamela J.
Abstract:: BACKGROUND: The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational...
Resource Type:: Article

Transcriptome assembly and analyses of gene expression in diploid wheat Triticum monococcum

Creator:: Fox, Samuel E., Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K., Elser, Justin, Leonard, Jeffery M., Sage, Abagail, Gresham, Cathy, Kerhornou, Arnaud, Bolser, Dan, McCarthy, Fiona, Kersey, Paul, Lazo, Gerard R., and Jaiswal, Pankaj
Abstract:: Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
Resource Type:: Dataset

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

Creator:: Priest, Henry D., Fox, Samuel E., Rowley, Erik R., Murray, Jessica R., Michael, Todd P., and Mockler, Todd C.
Abstract:: Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression...
Resource Type:: Article

Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

Creator:: Li, Chuan, Rudi, Heidi, Stockinger, Eric J., Cheng, Hongmei, Cao, Moju, Fox, Samuel E., Mockler, Todd C., Westereng, Bjorge, Fjellheim, Siri, Robnli, Odd Arne, and Sandve, Simen R.
Abstract:: Background: Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP) genes, fructosyltransferase (FST) genes, and many C-repeat binding factor (CBF) genes are Pooideae specific and important in low temperature responses. Here we used comparative...
Resource Type:: Article

Transcriptomic analysis using high-throughput sequencing and DNA microarrays

Creator:: Fox, Samuel E.
Abstract:: Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
Resource Type:: Dissertation

ScholarsArchive@OSU

A single generation of domestication heritably alters the expression of hundreds of genes

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Transcriptome assembly and analyses of gene expression in diploid wheat Triticum monococcum

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

Transcriptomic analysis using high-throughput sequencing and DNA microarrays

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