Systemic analysis of microarray data sets towards identifying genes regulating root development

Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation. It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.

Speciation with gene-flow in eastern North American red oaks (Quercus section Lobatae)

As foundational species, oaks (Quercus : Fagaceae) support the activities of both humans and wildlife. However, many oaks in North America are declining, a crisis exacerbated by the previous disappearance of other hard mast-producing trees. In addition, the economic demands placed on this drought-tolerant group may intensify if climate change extirpates other, relatively mesophytic species. Genetic tools can help address these management challenges. To this end, we developed a suite of 27 microsatellite markers, of which 22 are derived from expressed sequence tags (ESTs). Many of these markers bear significant homology to known genes and may be able to directly assay functional genetic variation. Markers obtained from enriched microsatellite libraries, on the other hand, are typically located in heterochromatic regions and should reflect demographic processes. Considered jointly, genic and genomic microsatellites can elucidate patterns of gene-flow and natural selection, which are fundamental to both an organism's evolutionary ecology and conservation biology. To this end, we employed the developed markers in an FST-based genome scan to detect the signature of divergent selection among the red oaks (Quercus section Lobatae). Three candidate genes with putative roles in stress responses demonstrated patterns of diversity consistent with adaptation to heterogeneous selective pressures. These genes may be important in both local genetic adaptation within species and divergence among them. Next, we used an isolation-with-migration model to quantify levels of gene-flow among four red oaks species during speciation. Both speciation in allopatry and speciation with gene-flow were found to be major drivers of red oak biodiversity. Loci playing a key role in speciation are also likely to be ecologically important within species