Abstract
Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
Highlights
The Ochrophyta, a monophyletic phylum within the Stramenopiles, are the most diverse algal group with secondary plastids of algal origin in terms of morphology, pigmentation and phylogeny[3,4]
The newly sequenced plastid genomes exhibit size, GC content, and gene content similar to previously sequence plastid genomes. Both genomes display the typical circular-mapping architecture and the presence of inverted repeat (IR) regions separated by a large single copy and a small single copy region
The IR copies are identical at the nucleotide sequence level except for one-nucleotide deletion in one of the psaC copies in Trachydiscus introducing a frame-shift into the coding sequence; this copy is probably a non-functional pseudogene
Summary
The Ochrophyta, a monophyletic phylum within the Stramenopiles (or Heterokonta), are the most diverse algal group with secondary plastids of algal origin in terms of morphology, pigmentation and phylogeny[3,4]. The position of the root of the ochrophyte phylogeny remains unknown Despite these uncertainties and sometimes lack of statistical support, many different putative groupings of ochrophyte classes have been proposed[11]. The second conceptual framework builds on a growing amount of data suggesting that a red algal plastid was acquired by one “chromalveolate” lineage, from which it spread to others through a series of higher-order tertiary or even quaternary endosymbioses (see, e.g.,21–25). This scenario has recently been dubbed the “rhodoplex hypothesis”[26]. Higher-order endosymbiotic gains of plastids postulated by the rhodoplex hypothesis have only been conclusively demonstrated for some dinoflagellate lineages[2,27]
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