Index Catalog // ScholarsArchive@OSU

Assessing De Novo transcriptome assembly metrics for consistency and utility

Creator:: O’Neil, Shawn T. and Emrich, Scott J.
Abstract:: Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results: We simulated sequencing transcripts of Drosophila melanogaster. By assembling...
Resource Type:: Article
Full Text:: ://www.biomedcentral.com/1471-2164/14/465 RESEARCH ARTICLE Open Access Assessing De Novo transcriptome assembly metrics

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: untitled Genome-Wide Profiling and Analysis of Arabidopsis

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Creator:: Traeger, Stefanie, Altegoer, Florian, Freitag, Michael, Gabaldon, Toni, Kempken, Frank, Kumar, Abhishek, Marcet-Houben, Marina, Poggeler, Stefanie, Stajich, Jason E., and Nowrousian, Minou
Abstract:: Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely...
Resource Type:: Article
Full Text:: -Universität Bochum, Bochum, Germany, 2 Center for Genome Research and Biocomputing, Department of

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Creator:: Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.
Abstract:: The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
Resource Type:: Article
Full Text:: America, 3 Center for Genome Research & Biocomputing, Oregon State University, Corvallis, Oregon, United

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:: Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.
Abstract:: Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...
Resource Type:: Article
Full Text:: of America, 4 Center for Genome Research and Biocomputing, Oregon State University, Corvallis

Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes

Creator:: Clark, Katie A., Howe, Dana K., Gafner, Kristin, Kusuma, Danika, Ping, Sita, Estes, Suzanne, and Denver, Dee R.
Abstract:: Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals...
Resource Type:: Article
Full Text:: Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis

The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters

Creator:: Connolly, Lanelle R., Smith, Kristina M., and Freitag, Michael
Abstract:: The cereal pathogen Fusarium graminearum produces secondary metabolites toxic to humans and animals, yet coordinated transcriptional regulation of gene clusters remains largely a mystery. By chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq) we found that regions with secondary metabolite clusters are enriched for trimethylated histone H3 lysine 27 (H3K27me3), a...
Resource Type:: Article

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Creator:: Mi, Gu, Di, Yanming, Emerson, Sarah, Cumbie, Jason S., and Chang, Jeff H.
Abstract:: When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...
Resource Type:: Article
Full Text:: , Oregon, United States of America, 4 Center for Genome Research and Biocomputing, Oregon State University

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

Creator:: Hicks, Kiley A., Howe, Dana K., Leung, Aubrey, Denver, Dee R., and Estes, Suzanne
Abstract:: In We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5 Delta) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial...
Resource Type:: Article
Full Text:: , Portland, Oregon, United States of America, 2 Department of Zoology and Center for Genome Research and

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Creator:: Fischer, Sylvia E. J., Montgomery, Taiowa A., Zhang, Chi, Fahlgren, Noah, Breen, Peter C., Hwang, Alexia, Sullivan, Christopher M., Carrington, James C., and Ruvkun, Gary
Abstract:: Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...
Resource Type:: Article
Full Text:: , 2 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United

ScholarsArchive@OSU

Assessing De Novo transcriptome assembly metrics for consistency and utility

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes

The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

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