Comparative Plastid Genomics of Non-Photosynthetic Chrysophytes: Genome Reduction and Compaction

Spumella-like heterotrophic chrysophytes are important eukaryotic microorganisms that feed on bacteria in aquatic and soil environments. They are characterized by their lack of pigmentation, naked cell surface, and extremely small size. AlthoughSpumella-like chrysophytes have lost their photosynthetic ability, they still possess a leucoplast and retain a plastid genome. We have sequenced the plastid genomes of three non-photosynthetic chrysophytes,Spumellasp. Baeckdong012018B8,Pedospumellasp. Jangsampo120217C5 andPoteriospumella lacustrisYongseonkyo072317C3, and compared them to the previously sequenced plastid genome of Spumella sp. NIES-1846 and photosynthetic chrysophytes. We found the plastid genomes ofSpumella-like flagellates to be generally conserved with respect to genome structure and housekeeping gene content. We nevertheless also observed lineage-specific gene rearrangements and duplication of partial gene fragments at the boundary of the inverted repeat and single copy regions. Most gene losses correspond to genes for proteins involved in photosynthesis and carbon fixation, except in the case ofpetF. The newly sequenced plastid genomes range from similar to 55.7 kbp to similar to 62.9 kbp in size and share a core set of 45 protein-coding genes, 3 rRNAs, and 32 to 34 tRNAs. Our results provide insight into the evolutionary history of organelle genomesviagenome reduction and gene loss related to loss of photosynthesis in chrysophyte evolution.