Fig. 1
From: POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes
An example visualization from POInTbrowse. Shown is a region of ten duplicated regions (“pillars”) with between 6 and 12 surviving genes from six species sharing the At-α polyploidy event. The view is centered on the selected gene from Arabidopsis thaliana, AT5G03330 (pink outline). Users control the visualization size, window size and the format of the downloaded gene trees from the top controls. The tree pictogram on the upper left gives the assumed species phylogeny, while the “Model” button gives a visualization of the duplicate loss model used for the event (including model parameters). At right, the “Key” button illustrates the color scheme while the “Stats” button gives the POInTbrowse version, the size of the current dataset and the sizes of all datasets currently in POInTbrowse. Users can navigate ½ frame left or right with the arrows or re-center the frame on a pillar by clicking on it. Hovering over a gene gives its chromosomal coordinates and its common name (if known). Gene names shown in blue link to the corresponding model organism gene database entry for that gene. The location of the current frame relative to the full set of pillars is shown with the red region in the blue-gray bar at the bottom. This bar can also be used for coarse navigation within the pillars of an event. The upper panel with some blue genes shows the less fractionated subgenome, the bottom, the more fractionated one (green). Light pink genes are fully retained as duplicates and the darker pink pillar illustrates a reciprocal gene loss. Pillars with a mix of duplicated and single-copy genes are shown in tan. Numbers at the top of each pillar are POInT’s confidence estimate (0.1) for the orthology relationships shown (see text). At the bottom of each pillar, the tree pictogram will download a gene tree with the corresponding orthology relationships for the genes in that pillar; the “CDS” button will download the coding sequences of the genes in question. A PDF version of the current window can be downloaded from the “PDF” button at right; the “Batch query” button opens a new window with the batch download interface