nucleomorph

GO:0033009 · Membrane organelle · Membrane bounded organelle · Proposed

A small, vestigial nucleus found in some plastids that derive from a eukaryotic endosymbiont. Observed in chlorarachniophytes and cryptomonads, which acquired their plastids from a green and red alga respectively. [GO:0033009]

Synonyms: residual endosymbiont nucleus; remnant endosymbiont nucleus

Part of: plastid (GO:0009536)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
nucleomorph chromosomes	Dna	part of	Reviewed label only (reviewed name; no accession asserted)			ESSENTIAL	Highly reduced linear chromosomes that carry the residual eukaryotic endosymbiont nuclear genome inside the nucleomorph. `DOI:10.1038/nature11681` Curtis et al. 2012 compared cryptophyte and chlorarachniophyte algae whose remnant endosymbiont nuclei retain small essential-gene residues. `DOI:10.1186/1471-2164-15-374` Tanifuji et al. 2014 sequenced the three linear chromosomes of the Lotharella oceanica nucleomorph genome.

Taxonomic distribution

NCBITaxon:3027 Cryptophyceae — COMMON: Cryptophyte nucleomorphs are residual red-algal nuclei inside secondary plastids. [DOI:10.1038/nature11681]
NCBITaxon:29197 Chlorarachniophyceae — COMMON: Chlorarachniophytes retain green-algal-derived nucleomorphs within their complex plastids. [DOI:10.1186/1471-2164-15-374]

Canonical examples

NCBITaxon:55529 Guillardia theta — Cryptophyte model whose nucleomorph and chloroplast replication were followed through the cell cycle. [DOI:10.1038/s41598-017-02668-2]
NCBITaxon:227086 Bigelowiella natans — Chlorarachniophyte model compared with Guillardia theta to explain why a small residue of essential genes remains locked in each nucleomorph. [DOI:10.1038/nature11681]

Functions

reduced endosymbiont genome maintenance — The nucleomorph houses the compact remnant genome of an engulfed eukaryotic algal endosymbiont inside a secondary plastid.
- DOI:10.1038/nature11681 Curtis et al. 2012 found that the Guillardia theta and Bigelowiella natans nucleomorphs retain small sets of essential genes.
nucleomorph genome replication — The nucleomorph genome is replicated once per Guillardia theta cell cycle in coordination with plastid replication.
- DOI:10.1038/s41598-017-02668-2 Onuma et al. 2017 measured host nuclear and nucleomorph DNA synthesis timing in the cryptophyte Guillardia theta.

Mechanism graphs

Nucleomorphs retain reduced endosymbiont chromosomes (FUNCTION)

Cryptophyte and chlorarachniophyte nucleomorphs house highly reduced endosymbiont-derived chromosomes inside secondary plastids and replicate them once during the host-cell cycle.

Subject	Predicate	Object	Evidence
nucleomorph chromosomes	are housed in	nucleomorph	`DOI:10.1186/1471-2164-15-374` Tanifuji et al. 2014 resolved the Lotharella oceanica nucleomorph genome as three linear chromosomes.
nucleomorph	is part of	plastid	`GO:0033009` GO:0033009 defines nucleomorphs as vestigial nuclei found in plastids derived from eukaryotic endosymbionts.
nucleomorph chromosomes	encode	residual essential endosymbiont genes	`DOI:10.1038/nature11681` Curtis et al. 2012 compared Guillardia theta and Bigelowiella natans and argued that a residue of essential genes remains locked in the nucleomorph.
nucleomorph chromosomes	replicate through	nucleomorph DNA replication	`DOI:10.1038/s41598-017-02668-2` Onuma et al. 2017 measured the timing of nucleomorph DNA synthesis during the Guillardia theta cell cycle.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral groundings for nucleomorph chromosomes, the nucleomorph envelope, and any conserved nucleomorph pore or division machinery. This first nucleomorph record curates the directly sequenced residual chromosomes as reviewed-label-only because generic chromosome terms are broader than nucleomorph chromosomes, and leaves lipid-envelope and protein-machinery composition unmodeled until exact cross-lineage constituent classes are verified.

Evidence

GO:0033009 Gene Ontology cellular-component term for nucleomorph.
DOI:10.1038/nature11681 Curtis et al. 2012, 'Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs', Nature.
DOI:10.1038/s41598-017-02668-2 Onuma, Mishra and Miyagishima 2017, 'Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta', Scientific Reports.
DOI:10.1186/1471-2164-15-374 Tanifuji et al. 2014, 'Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica', BMC Genomics.

Curation history

2026-09-11T16:27:16Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-11T16:28:12Z codex · EXPANDED_RECORD — Added intracellular-organelle parentage, plastid parthood, nucleomorph synonymy and chromosome component curation, cryptophyte and chlorarachniophyte scope, Guillardia and Bigelowiella examples, reduced-genome and replication functions, a nonmechanistic nucleomorph-genome graph, and an envelope-component TODO.
2026-09-11T16:31:08Z codex · FIXED_ID_LABEL_MISMATCH — Renamed the GO:0009536 graph node from secondary_plastid to plastid to match the canonical GO label.
2026-09-11T16:37:55Z codex · ADDRESSED_REVIEW_ISSUES — Addressed review issues #519 and #520 by marking nucleomorph chromosomes reviewed-label-only and broadening the open TODO to cover exact chromosome grounding.

Source: data/structures/membrane_organelle/nucleomorph.yaml