Abstract
Thraustochytrids, diverse marine unicellular protists encompassing over 10 recognised genera, are renowned for synthesising polyunsaturated fatty acids (PUFAs), with content and composition varying substantially across genera. While PUFAs are known to be produced via PUFA synthase (PUFA‐S) and/or elongase/desaturase (ELO/DES) pathways, the distinctions in genes involved remain unexplored. This study analysed PUFA biosynthetic genes in 19 thraustochytrid strains across six genera, categorising them into four types. Type I exclusively utilises the ELO/DES pathway, Type II employs both PUFA‐S and complete ELO/DES pathways, while Types III and IV primarily rely on PUFA‐S, with Type III lacking the canonical Δ9 desaturase and Type IV missing most desaturase and elongase enzymes. Notably, the Δ9 desaturase and ATP‐citrate lyase ( ACLY ) are exclusive to Types I and II, while β‐carotene hydroxylase ( CrtZ ) is absent in these types. ACLY absence suggests alternative acetyl‐CoA supply pathways in Types III and IV, whereas CrtZ absence implies either a lack of specific xanthophylls or alternative biosynthetic pathways in Types I and II. Synteny analysis revealed conserved genomic organisation of PUFA biosynthetic genes, indicating a shared evolutionary trajectory. This study provides insights into the genetic diversity underlying PUFA biosynthesis in thraustochytrids, while proposing putative evolutionary pathways for the four lineages.