A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research

Global warming will jeopardize the persistence and genetic diversity of many species. Assisted colonization, or the movement of species beyond their current range boundary, is a conservation strategy proposed for species with limited dispersal abilities or adaptive potential. However, species that rely on photoperiodic and thermal cues for development may experience conflicting signals if transported across latitudes. Relocating multiple, distinct populations may remedy this quandary by expanding genetic variation and promoting evolutionary responses in the receiving habitat--a strategy known as assisted gene flow. To better inform these policies, we planted seeds from latitudinally distinct populations of the annual legume, Chamaecrista fasciculata, in a potential future colonization site north of its current range boundary. Plants were exposed to ambient or elevated temperatures via infrared heating. We monitored several life history traits and estimated patterns of natural selection to determine the adaptive value of plastic responses. To assess the feasibility of assisted gene flow between phenologically distinct populations, we counted flowers each day and estimated the degree of temporal isolation between populations. Increased temperatures advanced each successive phenological trait more than the last, resulting in a compressed life cycle for all but the southern-most population. Warming altered patterns of selection on flowering onset and vegetative biomass. Population performance was dependent on latitude of origin, with the northern-most population performing best under ambient conditions and the southern-most performing most poorly, even under elevated temperatures. Among-population differences in flowering phenology limited the potential for genetic exchange among the northern- and southern-most populations. All plastic responses to warming were neutral or adaptive; however, photoperiodic constraints will likely necessitate evolutionary responses for long-term persistence, especially when involving populations from disparate latitudes. With strategic planning, our results suggest that assisted colonization and assisted gene flow may be feasible options for preservation.

Summary1. In plants, the temporal pattern of floral displays, or display schedules, delimits an individual's mating opportunities. Thus, variation in the shape of display schedules can affect the degree of population synchrony and the strength of phenological assortative mating by flowering onset date. A good understanding of the mechanisms regulating the timing of flowering onset has been developed, but we know less about factors influencing subsequent patterns of floral display. 2.We observed unusual multimodal display schedules in temperate populations of the annual legume Chamaecrista fasciculata. Here, we ask whether 'flowering pulses' are simultaneous among individuals and populations and explore potential underlying mechanisms and consequences of pulsed flowering.3. We monitored daily flower production for individual plants from genetically divergent populations during a series of field experiments that manipulated three potential influencers of display schedule shape: average daily temperature, pollinator availability and watering schedules. We measured floral longevity to isolate the contributions of flower retention and flower deployment to display schedules. We assessed relationships between flowering and environmental variables and compared estimates of population synchrony, individual synchrony and the strength of assortative mating with those of 29 unimodally flowering species from the area. 4.We observed simultaneous flowering pulses in all experiments, with peaks aligned among individuals and populations despite variation in flowering onset and/or duration. Pulses were not the result of increases in average temperature, pollinator availability or variation in watering schedules. Seasonal fluctuations in temperature correlated with floral longevity and flower deployment, suggesting that the shape of display schedules may be plastic in response to fluctuations in temperature. Average population and individual synchrony differed only slightly from those of the species with unimodal schedules, while the average strength of assortative mating for flowering onset date was strongly reduced (0.21 in C. fasciculata vs. 0.35 for the 29 other species).5. Synthesis. Researchers should take caution in assuming that components of display schedules are genetically or developmentally correlated with flowering onset. Variation in the shape of display schedules can influence patterns of gene flow within or between populations, with potential effects on the strength of phenological assortative mating and subsequent responses to selection.

High throughput sequencing has opened the doors for investigators to probe genetic variation present in large populations of organisms. In plants, the 1001 Genomes Project (1001genomes.org) is one such effort that sought to characterize the extant worldwide variation in Arabidopsis thaliana for future analyses to compare and draw upon. We developed a web application that accesses the 1001 Genomes database called The Variant Viewer, for investigators to view variants in any A. thaliana gene and within gene families. These variants may be visualized in the context of alignments of queried genes, across splice isoforms of these genes and in relation to conserved domains.