A Cnidaria-specific core single-copy ortholog resource (CCO), built from the same 153-proteome OrthoFinder run that powers the gene-family pages, with the species × orthogroup presence/absence matrix released alongside it. Where BUSCO scores a genome against a curated lineage, this defines the core on CnidoSite's own taxonomic sampling and lets you re-threshold it.
All 153 proteomes in the CnidoSite OrthoFinder run (148 cnidarians plus
five non-cnidarian outgroups: four sponges and a ctenophore), clustered into 300,793
orthogroups. Orthogroup membership is taken as OrthoFinder produced it; the only correction
applied is that copy number counts distinct genes, collapsing multiple transcripts of
one gene model (a trailing .t1, .t2, ...) into a single copy. That
matters more than it sounds: without it a genome with two isoforms of a single-copy gene looks
duplicated.
A cnidarian genome enters the high-quality set when BUSCO cnidaria_odb12 reports
≥90% complete against its proteome. That yields 60 genomes
(46 Hexacorallia, 10 Octocorallia, 4 Hydrozoa). Orthogroups are scored against this set. The two outgroup phyla are scored separately and
never counted as cnidarian.
busco_summary.high_quality. The site's own
high_quality flag is a separate and much stricter set — 15 genomes, all
≥91% — used elsewhere. This resource deliberately uses the 90% completeness cutoff
instead and stores it in its own column, core_species.busco90, so that a query
joining the two tables cannot silently pick up the wrong set. Of the 15 flagged genomes, 14
are inside these 60; the exception is Pachycerianthus multiplicatus,
which is not part of the OrthoFinder run at all and so is absent from this resource entirely.
An orthogroup's single-copy fraction is the share of the high-quality genomes in which it has exactly one gene. An orthogroup enters a tier when that fraction reaches the tier's cutoff: strict 90%, core 80%, extended 70%. Presence is implied — a single-copy genome is a present genome — but presence across all 148 cnidarians is reported separately, because a gene can be core in the high-quality set and still be missing from the more fragmented assemblies.
The five outgroups are the only way to root a matrix built from this resource, and they are
single-copy in only part of each tier, so core_og.tsv carries an
outgroup_single column. Filter on outgroup_single >= 3 to get the
rootable subset.
Two checks are reported on the overview tab. Against BUSCO: the majority of the
cnidaria_odb12 groups that reach ≥90% single-copy over the high-quality genomes
have a member inside a CCO orthogroup, and a large share of CCO member genes carry a BUSCO
assignment — the CCO set is enriched for the conserved genes BUSCO tracks, not a
disjoint set.
Against taxonomy: each supermatrix was run through FastTree (-nosupport) as a
usability check, and the class-level clades were scored for monophyly. Cubozoa, Hydrozoa,
Octocorallia and Scyphozoa come out monophyletic on all three tiers, and the five outgroup
proteomes are monophyletic on the core tier (130 taxa). The strict tier (135 taxa) and the
extended tier (144 taxa) additionally recover Myxozoa, but on those two the outgroups do
not stay together. Hexacorallia is not recovered on any tier, and Staurozoa is
represented by a single genome, so its placement means nothing. These are approximate,
unrooted, support-free trees of a matrix that has not been trimmed or model-selected —
read them as evidence that the resource is usable, never as a phylogeny. Deep relationships
among the classes should not be taken from them. The trees themselves are in the download
section.
Please cite CnidoSite and the OrthoFinder run described on the gene family pages. The tier cutoffs, BUSCO comparison and the presence/absence matrix are described in the manuscript's core-ortholog section.
