Satellite Model Organisms

Overview

This project collects gene reviews for satellite model organisms — species
that are studied primarily in comparison to an established model organism
database (MOD) reference, but are not themselves a MOD sensu stricto. They are
the comparison points that give a reference MOD its evolutionary and functional
context: close relatives used for comparative genomics, evo-devo, and
trait-evolution studies.

The canonical example here is the nematodes orbiting Caenorhabditis elegans.
Pristionchus pacificus is explicitly described in the literature as a
"satellite model organism" to C. elegans, and Caenorhabditis briggsae is the
standard congeneric comparison species for C. elegans genetics and genomics.
Their annotation status is uneven: many genes are known only through orthology to
the reference MOD, which makes them good targets for AI-assisted review that
synthesizes literature with comparative inference.

What counts as a "satellite" here

• Comparative, not reference. The species is used to interpret a reference
  MOD (e.g. C. elegans, D. melanogaster, S. cerevisiae), rather than being
  the primary reference itself.
• Not a MOD sensu stricto. It is not one of the established GO Consortium
  reference-genome MODs with a dedicated, fully-staffed curation database. (Some
  satellites — e.g. P. pacificus via pristionchus.org, C. briggsae via
  WormBase — have substantial resources, but are still studied chiefly as
  comparators.)
• Distinct from parasites. Parasitic / host-associated species are tracked
  separately in PARASITES. A species can be both a comparative
  model and a parasite (e.g. entomopathogenic nematodes); when in doubt, the
  parasite framing takes precedence for the gene biology and the satellite
  framing for the comparative-annotation angle. Cross-link rather than duplicate.

Species in scope

Species	UniProt code	Reference MOD	In repo?	Notes
Caenorhabditis briggsae	CAEBR	C. elegans (worm)	✅ 10 genes seeded (see below)	Standard congeneric comparator; sex-determination genes are the flagship comparative-evolution set
Pristionchus pacificus	PRIPA (NCBITaxon:54126)	C. elegans (worm)	✅ genes/PRIPA/oaz	Necromenic beetle associate; evo-devo "satellite model" for mouthpart plasticity

Other genera (e.g. comparative Drosophila species, Saccharomyces relatives)
may be added as gene reviews accrue.

Genes for review

• [x] CAEBR drd-5 — dopamine-receptor-family gene; reviewed (see
  genes/CAEBR/drd-5/).
• CAEBR sex-determination set — seeded as the flagship comparative-evolution
  batch (sex determination is the canonical C. briggsae vs C. elegans evo-devo
  story); annotations are PENDING review:
• [ ] tra-1 (Q17308) — Gli/Ci-family transcription factor, terminal global
  regulator of the sex-determination pathway (PE=1; has experimental annotation).
• [ ] tra-2 (Q17307) — membrane receptor-type regulator of sex
  determination (PE=1; has experimental annotations).
• [ ] fem-3 (Q8I8U6) — sex-determination protein FEM-3 (PE=1; has
  experimental annotations).
• [ ] she-1 (A8XDR5) — F-box "spermless hermaphrodites" protein, a
  C. briggsae-lineage-specific gene required for hermaphrodite spermatogenesis;
  no GO annotations yet (annotation gap — a good de-novo curation target).
• CAEBR other protein-level (PE=1) genes — the remaining C. briggsae
  entries with experimental protein-level evidence; seeded, annotations PENDING:
• [ ] cep-1 (A8WW61) — p53/p63/p73-family transcription factor
  (germline DNA-damage apoptosis); 31 GOA annotations.
• [ ] trr-1 (A8WTE8) — TRRAP-like transcription-associated protein.
• [ ] kin-1 (A8XW88) — cAMP-dependent protein kinase catalytic subunit (PKA).
• [ ] peb-1 (A8XJ98) — FLYWCH-type zinc-finger pharyngeal regulator
  (has an experimental annotation).
• [ ] ubl-1 (P37164) — ubiquitin-like / ribosomal eS31 fusion protein.
• [ ] PRIPA oaz (Q9NHZ4, ornithine decarboxylase antizyme) — seeded into
  genes/PRIPA/oaz/; annotations are PENDING review. This is the species' only
  reviewed (Swiss-Prot) entry; its 4 GOA annotations are all IBA/IEA (no
  experimental evidence).
• [ ] PRIPA developmental-plasticity / predatory-morph genes — TrEMBL-only;
  candidates for future review from literature + bioinformatics.

Status / next steps

• SCOPING. C. briggsae drd-5 + sex-determination set (tra-1, tra-2,
  fem-3, she-1) and P. pacificus oaz are present.
• C. briggsae has 582 reviewed entries; the protein-level (PE=1)
  experimentally-characterized ones cluster on sex determination, which is why
  that set was chosen as the first comparative batch.
• Annotation availability (UniProt, 2026-06): PRIPA has just 1 reviewed
  (Swiss-Prot) entry — Q9NHZ4 (OAZ_PRIPA, ornithine decarboxylase antizyme,
  142 aa), now seeded as genes/PRIPA/oaz/ — alongside ~26,000 unreviewed TrEMBL
  entries. The classic developmental-plasticity / predatory-morph genes are all
  TrEMBL-only, so seeding those means working from unreviewed accessions.
• Next: complete the PENDING annotation review of PRIPA oaz, and decide
  whether to pull in TrEMBL plasticity genes (e.g. the eud-1/sulfatase morph
  switch) backed by literature + bioinformatics.
• Where a satellite gene is annotated only by orthology to the reference MOD,
  record in the review whether the comparative inference is supported by direct
  evidence in the satellite species.

Related projects

• PARASITES — parasitic / host-associated organisms (some
  nematodes overlap with this project).
• CEPHALOPOD, TARDIGRADE_STRESS_RESPONSE
  — other non-MOD organism gene-review collections.