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Teleaulax amphioxeia  is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate  Dinophysis caudata  through the ciliate  Mesodinium rubrum  in the marine food web. To better understand the genomic characteristics of  T .  amphioxeia , we have sequenced and analyzed its plastid genome. The plastid genome sequence of  T .  amphioxeia  is similar to that of  Rhodomonas salina , and they share significant synteny. This sequence exhibits less similarity to that of  Guillardia theta , the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of  T .  amphioxeia  is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene ( dna X) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in  R .  salina . On the other hand, the  psb N gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.

The Plastid Genome of the Cryptomonad Teleaulax amphioxeia