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.

Centre for Algology and Biorefinery Research Centre of Competence Institute of Botany Czech Academy of Sciences Dukelská 135 379 82 Třeboň Czech Republic

Département de Biochimie Centre Robert Cedergren Université de Montréal 2900 Boulevard Edouard Montpetit Montréal Québec H3C 3J7 Canada

HudsonAlpha Institute for Biotechnology 601 Genome Way NW Huntsville Alabama 35806 USA

Institute of Molecular Genetics Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic

Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 31 370 05 České Budějovice Czech Republic

Integrated Microbial Biodiversity Program Canadian Institute for Advanced Research Toronto M5G 1Z8 Canada

Monterey Bay Aquarium Research Institute Moss Landing CA 95039 USA

University of Ostrava Faculty of Science Department of Biology and Ecology Life Science Research Centre Chittussiho 10 710 00 Ostrava Czech Republic

University of South Bohemia Faculty of Science Branišovská 1760 370 05 České Budějovice Czech Republic

US Department of Energy Joint Genome Institute Walnut Creek California 94598 USA

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