Macrosynteny Analysis

Millepora alcicornis vs Millepora complanata (Hydrozoa × Hydrozoa)

Interactive Oxford grid of conserved linkage groups, over 2,732 BUSCO single-copy orthologs shared by the two species. X axis = Millepora alcicornis, Y axis = Millepora complanata; chromosomes are ordered as inferred by macrosyntR, not by their natural order. The plot opens fitted to the window and in cell view: one cell per chromosome pair, tinted by its linkage group and labelled with its anchor count, so the conserved blocks and their sizes are readable at a glance. Zoom in (+, Ctrl + mouse wheel — ⌘ + wheel on a Mac — or a double-click) and it switches to anchor view, one dot per anchor; Fit returns to the whole grid, and whatever you point at stays in place while zooming. Hover a cell for its chromosome pair, anchor count, significance and ρ; click it to zoom into that block. Hover a dot for its BUSCO and gene, and click it to pin that panel to the figure.

Reading the grid: it has two zoom levels, and switches between them on its own. In cell view each cell is one sequence pair (chromosome, scaffold or contig) — its tint is the linkage group, the number inside is how many anchors that pair shares, and a white cell means the two sequences have no anchor in common. Zoom in past ~5 px per anchor and it becomes anchor view: one dot per anchor, which is where you look up an individual gene. Drag to pan; zoom with the − / + buttons, Ctrl + mouse wheel (⌘ + wheel on a Mac) or a double-click — zooming keeps the point under the pointer in place, so whatever you aim at stays put. Fit shows the whole grid, 1:1 puts one anchor on one pixel and Full screen gives it the whole window. Hover a cell or a dot for details; clicking a cell zooms to that block, clicking a dot pins its panel open so its gene links can be clicked. Esc (or a click on empty space) closes a pinned panel.

Two things worth knowing about the axes. Fragmented assemblies: some of these genomes are still in thousands of unplaced scaffolds, and a handful of that species’ scaffolds carry almost all of the anchors. The chromosomes, scaffolds or contigs that hold the anchors are drawn and named one by one; everything past Labels per axis is merged into the light band at the end of the axis, labelled other with how many sequences and anchors it holds. Nothing is thrown away — every anchor in that band is still plotted, and in cell view each sequence on the other axis gets one block showing how many anchors it shares with the whole band — but with Fill canvas on, the band is squeezed to keep it from eating the axis, so it is then not to scale. Raise Labels per axis to give more of it its own column. Fill canvas (on by default) scales each axis to the panel separately, which is what makes a square grid use a wide screen instead of sitting in the middle of it with white space either side; the price is that the two axes are then at different scales. Uncheck it for the equal-scale version — the grid then goes back to being drawn to scale on both axes (the band included), which is the honest picture for a pair of chromosome-level assemblies.