Life Sciences Commons^™

Genomic Neighborhoods For Arabidopsisretrotransposons: A Role For Targeted Integration In The Distribution Of The Metaviridae, Brooke D. Peterson-Burch, Dan Nettleton, Daniel F. Voytas

Dan Nettleton

Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.

Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution …

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from …

Transcriptomic And Anatomical Complexity Of Primary, Seminal, And Crown Roots Highlight Root Type-Specific Functional Diversity In Maize (Zea Mays L.), Huanhuan Tai, Xin Lu, Nin Opitz, Caroline Marcon, Anja Paschold, Andrew Lithio, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across …

Non-Syntenic Genes Drive Rtcs-Dependent Regulation Of The Embryo Transcriptome During Formation Of Seminal Root Primordia In Maize (Zea Mays L.), Huanhuan Tai, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo …

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism And Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, Ling Li

Dan Nettleton

Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; …