Core Orthologs

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.

224core orthogroups 14strict tier 1,017extended tier 60genomes at ≥90% BUSCO 153proteomes scored 136,050member genes
Overview Core orthogroups Presence / copy number Species Download Methods

What this resource is

For every orthogroup in the CnidoSite OrthoFinder run we report the fraction of genomes in which it is present and the fraction in which it is single-copy. An orthogroup enters a tier when its single-copy fraction among the high-quality genomes clears that tier's cutoff. The tiers are cumulative, so strict is a subset of core, which is a subset of extended.

TierSingle-copy inOrthogroups Typical use
strict ≥90% of the 60 high-quality genomes 14 Highest-confidence markers; concatenation with almost no missing data.
core ≥80% 224 The default marker set for phylogenomics and cross-species comparison.
extended ≥70% 1,017 Maximum gene count; expect more missing data and more copy-number decisions.
Why tiers rather than one number. No cutoff is right for every use, so the full per-orthogroup score table is downloadable and every table on this page can be re-filtered. The tier sizes are a property of cnidarian genomes, not of the pipeline: coral genomes in particular carry 20–43% duplicated BUSCOs, so genuinely single-copy genes are rarer here than the BUSCO group count suggests.

How this compares with BUSCO

The same question asked of the curated cnidaria_odb12 lineage, over the same 60 high-quality genomes — a BUSCO group counted as single-copy only where BUSCO called it Complete (not Duplicated) in that genome:

Single-copy inBUSCO cnidaria_odb12 CCO orthogroups
100% of genomes 1 of 3,203 0
≥95% 36 of 3,203 —
≥90% 174 of 3,203 14
≥80% 982 of 3,203 224
This is the point of the resource. Even the curated lineage is not universally single-copy across these genomes: not one of its 3,203 groups is single-copy in all 60 high-quality genomes. The two sets are complementary rather than competing — 66% of the BUSCO groups that reach ≥90% single-copy do have members inside a CCO orthogroup, and 48% of CCO member genes carry a BUSCO assignment, so the CCO set is enriched for exactly the conserved genes BUSCO tracks.

Getting started

  • Browse the core orthogroups — search by annotation, filter by tier, and follow any row through to its gene family page and gene tree.
  • Inspect the presence/absence matrix — every genome against every core orthogroup, coloured by copy number.
  • Download the matrices, the core gene sequences, and ready-made concatenated supermatrices with partition files.
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