Red-Algal Endosymbiotic Gene Transfer in Secondary Plastid-Bearing Dinoflagellates: A Systematic Review and Phylogenomic Evidence Map

Abstract

The plastids of peridinin-containing dinoflagellates ultimately derive from a red alga acquired by secondary endosymbiosis, an event that required extensive endosymbiotic gene transfer (EGT) from the endosymbiont to the host nucleus. Although many individual studies have recovered a red-algal phylogenetic signal in nucleus-encoded, plastid-targeted dinoflagellate proteins, this evidence remains scattered across genome papers, transcriptome surveys, plastid-proteome predictions and single-gene phylogenies, and has never been compiled systematically. Conducted and reported in accordance with the PRISMA 2020 guideline adapted for evolutionary genomics, this systematic review aimed to map and grade that evidence at the level of individual genes, lineages and functional categories. Bibliographic databases and sequence repositories, including Web of Science, Scopus, PubMed, MMETSP and EukProt, were searched up to 31 January 2026, and a four-tier evidence-grading scheme (strong, moderate, weak, ambiguous) together with a phylogenomic risk-of-bias appraisal was applied. Twenty-four studies met the eligibility criteria. The strongest and most consistent red-algal signals were recovered among nucleus-encoded proteins of the photosynthetic electron-transport chain, the Calvin–Benson cycle, tetrapyrrole and carotenoid biosynthesis, and plastid gene expression, consistent with a chromalveolate origin of the peridinin plastid. Peridinean lineages carried the clearest red-derived signal, whereas haptophyte-derived (Kareniaceae) and diatom-derived (dinotom) lineages showed a younger layer of donor-specific ancestry that frequently obscured the original red signal. The number of recovered EGT candidates was also an order of magnitude greater in secondary than in tertiary plastid contexts.