Index Catalog // ScholarsArchive@OSU

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Creator:: Cronn, Richard, Liston, Aaron, Parks, Matthew, Gernandt, David S., Shen, Rongkun, and Mockler, Todd
Abstract:: Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence...
Resource Type:: Article
Full Text:: , David S. Gernandt, Rongkun Shen and Todd Mockler Multiplex sequencing of plant chloroplast genomes

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:: . Sullivan 1,2 , Jason S. Cumbie 1,2 , Scott A. Givan 1,2 , James C. Carrington 1,2* 1 Center for Genome

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: . Kasschau1, Elisabeth J. Chapman1,2, Christopher M. Sullivan1, Jason S. Cumbie1, Scott A. Givan1, Theresa F

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Creator:: Fahlgren, Noah, Sullivan, Christopher M., Kasschau, Krisitin D., Chapman, Elisabeth J., Cumbie, Jason S., Montgomery, Taiowa A., Gilbert, Sunny D., Dasenko, Mark, Backman, Tyler W. H., Givan, Scott A., and Carrington, James C.
Abstract:: The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these methods have been limited by several factors, including representational artifacts and lack of established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing and...
Resource Type:: Article
Full Text:: ,1,2 KRISTIN D. KASSCHAU,1,2 ELISABETH J. CHAPMAN,1,2,3 JASON S. CUMBIE,1,2 TAIOWA A. MONTGOMERY,1,2

Monitoring soil moisture and temperature impacts on soilborne fusarium diseases in processing vegetable cropping systems

Creator:: Buckland, Kristine and Ocamb, Cynthia M.
Abstract:: Sweet corn and snap bean production, amongst other vegetable crops grown in the Willamette Valley of Oregon, are impacted by soilborne diseases caused by Fusarium species. The decline in sweet corn yields due to Fusarium crown and stalk node rot as well as root rot in snap bean and sweet...
Resource Type:: Technical Report
Full Text:: . Also many thanks to Tim Flodquist, Mariah Dietrich, Taylor A. Bates, Alexandria S. Montgomery, Darby D

Plastome phylogenomics in the genus Pinus using massively parallel sequencing technology

Creator:: Parks, Matthew Benjamin
Abstract:: This thesis summarizes work completed over the previous four years primarily focusing on chloroplast phylogenomic inquiry into the genus Pinus and related Pinaceae outgroups using next-generation sequencing on Illumina platforms. During the time of our work, Illumina sequence read lengths have essentially been limited to 25 to 100 base pairs,...
Resource Type:: Dissertation
Full Text:: Gernandt et al. (2005). 9 LITERATURE CITED Asif M, Mantri S, Sharma A

Conservation genetics of Kincaid's lupine : a threatened plant of western Oregon and southwest Washington grasslands

Creator:: Severns, Paul M.
Abstract:: Kincaid's lupine (Lupinus oreganus Heller) is a federally listed threatened species native to remnant grassland of western Oregon and southwestern Washington, and is the primary larval host plant of a once thought extinct butterfly, Plebejus icarioides fenderi Macy. Past studies concerning Kincaid's lupine reproduction suggested that populations may suffer reductions...
Resource Type:: Dissertation
Full Text:: , Emma Bradford, Tri Tran, Mariah Parker-deFenix, and Stephanie McKnight whose aid in the lab made my

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

Creator:: Lee, Hanna, Yoo, Seong Jeon, Lee, Jeong Hwan, Kim, Wanhui, Yoo, Seung Kwan, Fitzgerald, Heather, Carrington, James C., and Ahn, Ji Hoon
Abstract:: Flowering is the primary trait affected by ambient temperature changes. Plant microRNAs (miRNAs) are small non-coding RNAs playing an important regulatory role in plant development. In this study, to elucidate the mechanism of flowering-time regulation by small RNAs, we identified six ambient temperature-responsive miRNAs (miR156, miR163, miR169, miR172, miR398 and...
Resource Type:: Article
Full Text:: , Vol. 38, No. 9 3081–3093 doi:10.1093/nar/gkp1240 � The Author(s) 2010. Published by Oxford University

An experimental reintroduction of Pleuropogon oregonus, a rare wetland grass native to Oregon

Creator:: Groberg, Matthew G.
Abstract:: Pleuropogon oregonus Chase is a rare wetland grass endemic to eastern Oregon. The species is composed of two widely separated populations, one in Lake County and one in Union County. In order to reduce the risk of extinction, the Oregon Department of Agriculture Native Plant Conservation Program initiated several reintroduction...
Resource Type:: Masters Thesis
Full Text:: , or fragmentation (Gustafson et al. 2002). Global climate change presents unique challenges to

Studies to facilitate reintroduction of golden paintbrush (Castilleja levisecta) to the Willamette Valley, Oregon

Creator:: Lawrence, Beth A.
Abstract:: Golden paintbrush (Castilleja levisecta Greenman) historically inhabited the prairies of the Willamette Valley, Oregon. However, this Pacific Northwest endemic is currently restricted to eleven sites in the Puget Trough of Washington and British Columbia. Recovery criteria call for the establishment of new populations throughout the species historic range, including the...
Resource Type:: Masters Thesis
Full Text:: 3 WA r~ N (!) l OR A 8 outh Puget Trough_,,.,----: Rocky Prairie a 50 ]QO b so Ml.fS • 0 }S

ScholarsArchive@OSU

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Monitoring soil moisture and temperature impacts on soilborne fusarium diseases in processing vegetable cropping systems

Plastome phylogenomics in the genus Pinus using massively parallel sequencing technology

Conservation genetics of Kincaid's lupine : a threatened plant of western Oregon and southwest Washington grasslands

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

An experimental reintroduction of Pleuropogon oregonus, a rare wetland grass native to Oregon

Studies to facilitate reintroduction of golden paintbrush (Castilleja levisecta) to the Willamette Valley, Oregon

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