Project description:Next-generation sequencing survey of maize plants exhibiting symptoms of maize lethal necrosis, collected from Kenyan and Ethiopian farmers in August 2014. Up to three samples per site were sequenced, and sites were separated by at least 10km. Data contains maize transcriptome and a variety of RNA viruses.
Project description:There are very few studies exploring the genetic diversity of tick-borne encephalitis complex viruses. Most of the viruses have been sequenced using capillary electrophoresis, however, very few viruses have been analyzed using deep sequencing to look at the genotypes in each virus population. In this study, different viruses and strains belonging to the tick-borne encephalitis complex were sequenced and genetic diversity was analyzed. Shannon entropy and single nucleotide variants were used to compare the viruses. Then genetic diversity was compared to the phylogenetic relationship of the viruses.
Project description:Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis-regulatory activity remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 maize inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and how transposons rewired the regulatory landscape. We found widespread chromatin accessibility variation associated with >4.6 million genetic variants with largely cell-type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most prevalent determinants of chromatin accessibility. Finally, integration of genetic variants associated with chromatin accessibility, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular context to alter maize flowering phenotypes.
Project description:Tar spot of maize, caused by Phyllachora maydis, is an emerging threat to crop production across the United States and Canada. Current effective management of the disease includes application of fungicides and use of partially resistant maize varieties. Several studies have focused on mapping of tar spot resistant loci from maize diversity panels. However, no additional analyses have been reported to further our understanding of the maize defense response to P. maydis. Therefore, prior to the availability of inoculation procedures, we performed transcriptome sequencing from maize leaf tissue exposed to P. maydis from a tar spot infested field and assessed differential gene transcript expression. Over the course of disease development, leaves were sampled at two timepoints: 10 days and 24 days post-exposure. Differentially expressed genes (DEGs) were determined by comparing gene transcript expression of the exposed samples to non-exposed controls at the respective timepoints.
Project description:Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal disease affecting preterm infants. NEC develops suddenly and is characterized by gut barrier destruction, an inflammatory response, intestinal necrosis and multi-system organ failure. There is currently no method for early NEC detection, and the pathogenesis of NEC remains unclear.
