Macrosynteny Analysis

Whole-genome synteny conservation between any two cnidarian species in CnidoSite. Conserved linkage groups (macrosynteny) are inferred from BUSCO single-copy orthologs used as cross-species anchor points: every pair of chromosomes is tested with a Fisher exact test, and significantly associated chromosomes are merged into linkage groups by greedy modularity clustering. Results are shown as an interactive Oxford grid — one dot per ortholog, coloured by its linkage group. Both within-class and between-class pairs can be compared: the two dropdowns below always list all species, grouped by class.

139 species 9,591 species pairs computed 395,668 ortholog anchors
Select Two Species to Compare
Both lists contain all species and are grouped by class (Hexacorallia, Hydrozoa, Octocorallia, …). Any two species may be compared, whether or not they belong to the same class — every one of the species pairs above has been computed. The comparison is undirected: which species goes on the X axis only flips the layout. When a pair has no significant linkage groups (for example the highly fragmented Myxozoa genomes), the result page says so instead of showing an empty plot.
→ Or view the all-pairs heatmap
Examples — the most complete comparisons
Species 1Species 2 Anchors Chr. pairs Significant Anchors in blocks Linkage groups Median ρ
Acropora_digitifera Acropora_palmata 3,154 14 14 100.0% 14 +1.00 view →
Porites_cylindrica Porites_rus 3,153 15 14 100.0% 14 +0.01 view →
Porites_cylindrica Porites_lutea 3,149 14 14 100.0% 14 +1.00 view →
Anthopleura_xanthogrammica Paracondylactis_sinensis 3,156 27 19 99.7% 19 +0.55 view →
Porites_cylindrica Porites_divaricata 3,143 14 14 100.0% 13 +0.01 view →
Porites_lutea Porites_rus 3,143 15 14 100.0% 14 +0.00 view →
Acropora_palmata Porites_cylindrica 3,153 26 14 99.6% 14 -0.07 view →
Condylactis_gigantea Paracondylactis_sinensis 3,142 20 19 100.0% 19 +1.00 view →
Acropora_palmata Porites_rus 3,148 27 14 99.6% 14 -0.53 view →
Porites_divaricata Porites_rus 3,136 15 14 100.0% 13 +1.00 view →
Acropora_palmata Porites_lutea 3,147 26 14 99.6% 14 +0.32 view →
Porites_divaricata Porites_lutea 3,135 14 14 100.0% 13 +1.00 view →
Species pairs with the richest linkage structure
Species 1Species 2AnchorsLinkage groupsAnchors in blocks
Acropora_acuminata Acropora_awi 2,952 26 85.6% view →
Acropora_acuminata Acropora_cervicornis 3,107 26 92.1% view →
Acropora_acuminata Acropora_cytherea 2,890 26 88.0% view →
Acropora_acuminata Acropora_gemmifera 2,954 26 87.8% view →
Acropora_acuminata Acropora_echinata 2,933 26 88.1% view →
Acropora_acuminata Acropora_florida 2,905 26 89.3% view →
How to read the Oxford grid
  • One dot = one pair of orthologs (the same BUSCO id, one copy in each species); its X/Y coordinates are the positions on the respective chromosomes.
  • Dots strung along the diagonal ⇒ that stretch of chromosome stayed collinear between the two species (conserved synteny).
  • Color = linkage group. A grey dot marks a chromosome pair that neither belongs to a linkage group nor is significant on its own.
  • Box = the chromosome block covered by a linkage group; all dots inside share one color, as inferred by macrosyntR's greedy modularity clustering on the significant association graph.
  • ρ: Spearman correlation of the anchor order within one chromosome block; ρ>0 means the two run in the same direction (collinear), ρ<0 means a whole-block inversion (inverted). This is an extra display metric computed here on top of the macrosyntR output.
  • The chromosome order on the axes is not the natural order but the order produced by macrosyntR's reordering: the largest linkage group first, then by anchor count per chromosome, so that homologous blocks end up adjacent.
Methods and citation. The macrosynteny analysis was run with macrosyntR: BUSCO cnidaria_odb12 single-copy orthologs are used as anchors, every chromosome pair is tested with a Fisher exact test (significant at q < 0.001 after BH correction), and linkage groups are then delineated on the significant association graph with igraph::cluster_fast_greedy. Please cite: El Hilali S., Copley R. R. macrosyntR: Drawing automatically ordered Oxford Grids from standard genomic files in R. bioRxiv (2023). doi:10.1101/2023.01.26.525673
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