Active Projects
Gene GC Content in Grasses
Grass genes have a bimodal GC distribution and a significant 5' to 3' GC gradient unlike the genes of most plant species that have a single, narrow GC distribution and a relatively uniform GC content across their genes. High gene GC content and strong negative 5' to 3' gradients in grasses strongly affect codon usage bias and have been shown to affect rates of transcription and translation. We have been funded by NSF to further characterize how gene GC content affects transcription and translation using rice as our model system.
Alkaloids in Catharanthus roseus
Catharanthus roseus (Madagascar periwinkle) contains a number of terpenoid indole alkaloids (TIAs) that serve as effective medicinal compounds. We are working with Carolyn Lee-Parsons and Erin Cram from Northeastern University on an NSF-funded project to examine ZCT transcriptional repressors of TIA synthesis in C. roseus. We will be analyzing gene expression data and performing coexpression analysis of RNA-seq data from hairy root tissues grown under a number of conditions that stimulate or repress the TIA pathway with the goal of identifying gene modules that are related to the synthesis of TIAs
Genome Annotation
Genome annotation is a strength of the Childs Lab. A former NSF-funded project (below) allowed us to work on the MAKER annotation pipeline. We are continuing that work with the annotation of numerous plant, fungal and oomycete genomes including Betula vulgaris, Fragaria vesca, Viola pubescens, Amanita bisporigera, Amanita phalloides, Ceratocystis fimbriata, Pseudoperonospora belbahrii and Pseudoperonospora humuli.
Past Projects
Abiotic Stress in Switchgrass
Kevin Childs was the lead investigator on a DOE funded project to examine drought and salt responses in switchgrass (Panicum virgatum). This project was a collaboration with Bingyu Zhao (Virginia Tech), Xunzhong Zhang (Virginia Tech) and C. Robin Buell (MSU). The goal of this project was to characterize within a wide range of switchgrass cultivars phenotypic diversity of responses to drought and salt stress. Physiological, metabolic and gene expression analyses were performed so that gene network analyses could be run with the aim of relating gene co-expression modules to physiological and metabolic phenotypes.
MAKER Annotation Pipeline
The lab was involved in an NSF funded project to extend and improve the MAKER gene annotation pipeline. This project was a collaboration with Mark Yandell (University of Utah), Ning Jiang (MSU), Shinhan Shiu (MSU) and Yanni Sun (MSU). Work was performed to extend the MAKER pipeline to better annotate grass genomes where the unusual gene GC distribution can negatively affect gene prediction. The lab was also involved in the annotation of new genomes from a number of species including Cleome violacea, Mimulus luteus, Zea mays cv. PH207 and Catharanthus roseus.