Macrosynteny Analysis

Every species pair in CnidoSite, compared with macrosyntR on BUSCO single-copy ortholog anchors. One cell = one species pair; the colour is the chosen statistic (default: the fraction of shared ortholog anchors that fall inside significant, conserved chromosome blocks). Click a cell to open the full Oxford grid for that pair. Cells cover within-class and between-class pairs alike.

139 species 9,591 pairs computed ⇄ Compare two species
0% 100% (light grey = no result for this pair: fewer than 30 shared anchors, or not computed yet)
Best-conserved species pairs
Species 1Species 2ClassAnchorsSignificant pairsAnchors in blocksLinkage groups
Acropora digitifera Acropora palmata Hexacorallia 3,154 14 100.0% 14 view →
Porites cylindrica Porites lutea Hexacorallia 3,149 14 100.0% 14 view →
Porites cylindrica Porites divaricata Hexacorallia 3,143 14 100.0% 13 view →
Porites divaricata Porites lutea Hexacorallia 3,135 14 100.0% 13 view →
Millepora alcicornis Millepora complanata Hydrozoa 2,732 15 100.0% 15 view →
Porites cylindrica Porites rus Hexacorallia 3,153 14 100.0% 14 view →
Porites lutea Porites rus Hexacorallia 3,143 14 100.0% 14 view →
Condylactis gigantea Paracondylactis sinensis Hexacorallia 3,142 19 100.0% 19 view →
Porites divaricata Porites rus Hexacorallia 3,136 14 100.0% 13 view →
Eunicella cavolini Eunicella verrucosa Octocorallia 3,099 18 100.0% 15 view →
Astrangia poculata Oculina arbuscula Hexacorallia 2,991 14 99.9% 14 view →
Oculina arbuscula Oculina patagonica Hexacorallia 3,050 14 99.9% 14 view →
Meandrina meandrites Oculina arbuscula Hexacorallia 3,116 14 99.9% 14 view →
Madracis auretenra Pocillopora verrucosa Hexacorallia 3,025 14 99.9% 14 view →
Leptoseris scabra Stephanocoenia intersepta Hexacorallia 2,980 14 99.8% 13 view →
Sorted by the fraction of anchors inside significant blocks; only pairs sharing ≥ 200 anchors are counted (the fraction is unstable when anchors are few).
Richest linkage structure
Species 1Species 2AnchorsLinkage groupsSignificant pairsAnchors in blocks
Acropora cervicornis Colpophyllia natans 3,145 26 215 88.6% view →
Acropora cervicornis Fimbriaphyllia ancora 3,138 26 206 89.7% view →
Colpophyllia natans Fimbriaphyllia ancora 3,133 26 204 89.3% view →
Acropora cervicornis Porites compressa 3,131 26 244 86.5% view →
Acropora cervicornis Acropora pulchra 3,128 26 121 96.9% view →
Acropora cervicornis Pocillopora acuta 3,127 26 199 86.3% view →
Colpophyllia natans Porites compressa 3,125 26 242 86.9% view →
Acropora cervicornis Porites lobata 3,122 26 259 81.1% view →
Acropora cervicornis Acropora tenuis 3,119 26 277 89.6% view →
Acropora cervicornis Dendrogyra cylindrus 3,118 26 231 86.3% view →
Fimbriaphyllia ancora Porites compressa 3,117 26 246 87.5% view →
Porites compressa Porites lobata 3,116 26 279 95.6% view →
Colpophyllia natans Porites lobata 3,115 26 272 83.4% view →
Colpophyllia natans Dendrogyra cylindrus 3,114 26 225 94.1% view →
Acropora tenuis Colpophyllia natans 3,110 26 271 78.4% view →
How to read this heatmap. The diagonal is a species against itself and is left blank. The darker the cell, the more / larger conserved chromosome blocks there are between the two genomes: a high frac_in_sig means most orthologs still sit together in blocks on chromosomes (a conserved karyotype), whereas a pale cell with many anchors means the orthologs are scattered over many chromosomes/contigs — the signature of an actively rearranged genome or a fragmented assembly (for example the reduced genomes of parasitic Myxozoa). Classes are marked with different side bars so within-class and between-class comparisons are easy to tell apart. The numbers come from macrosyntR: a Fisher exact test per chromosome pair, with significant pairs merged into linkage groups by igraph::cluster_fast_greedy.
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