Satellite Model Organisms

Bottom line: satellite model organisms are species studied mainly as
comparators to a reference model organism; here, the nematodes
Caenorhabditis briggsae and Pristionchus pacificus alongside
C. elegans. Most of their GO annotations are transferred by orthology, so we
reviewed them to see whether the comparative inference holds up. We reviewed
11 genes: 10 C. briggsae genes (drd-5, the sex-determination set tra-1,
tra-2, fem-3 and she-1, and five other protein-level entries) and oaz, the only
Swiss-Prot entry for P. pacificus. All 11 have been reviewed (the files still carry status: INITIALIZED). They cover 115
existing annotation rows (52 ACCEPT, 43 KEEP_AS_NON_CORE, 11
MARK_AS_OVER_ANNOTATED, 6 MODIFY, 3 REMOVE) and propose 4 NEW terms; she-1 had
no GO annotations and was curated from the literature. The open question is
whether to add the TrEMBL-only P. pacificus plasticity genes such as eud-1.

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

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

Genes for review

• [x] CAEBR drd-5 — short-chain dehydrogenase/reductase family enzyme ("dietary restriction down regulated"); 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); reviewed:
• [x] tra-1 (Q17308) — Gli/Ci-family transcription factor, terminal global
  regulator of the sex-determination pathway (PE=1; has experimental annotation).
• [x] tra-2 (Q17307) — membrane receptor-type regulator of sex
  determination (PE=1; has experimental annotations).
• [x] fem-3 (Q8I8U6) — sex-determination protein FEM-3 (PE=1; has
  experimental annotations).
• [x] 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; reviewed:
• [x] cep-1 (A8WW61) — p53/p63/p73-family transcription factor
  (germline DNA-damage apoptosis); 31 GOA annotations.
• [x] trr-1 (A8WTE8) — TRRAP-like transcription-associated protein.
• [x] kin-1 (A8XW88) — cAMP-dependent protein kinase catalytic subunit (PKA).
• [x] peb-1 (A8XJ98) — FLYWCH-type zinc-finger pharyngeal regulator
  (has an experimental annotation).
• [x] ubl-1 (P37164) — ubiquitin-like / ribosomal eS31 fusion protein.
• [x] PRIPA oaz (Q9NHZ4, ornithine decarboxylase antizyme) — seeded into
  genes/PRIPA/oaz/; reviewed. 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

• IN_PROGRESS. All 11 seeded genes are reviewed: C. briggsae drd-5, the
  sex-determination set (tra-1, tra-2, fem-3, she-1), five other PE=1
  genes, and P. pacificus oaz.
• 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: 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.

Slides

• Slides (Marp source: SATELLITE_MODEL_ORGANISMS-slides.md) — AI generated