Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 billion years ago and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (ca. 124 Mya) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mbp and 32,361 predicted gene models. A total of 291 chromatophore targeted proteins were predicted in silico, 206 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene co-expression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function (“dark” genes). We characterized diurnally rhythmic genes in this species and found that over 51% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion.

This paper describes the characteristics of microalgal strains that originated out of an 31 isolation and screening project included within the National Alliance for Advanced 32 Biofuels and Bioproducts (NAABB). The project's goal was to identify new potential 33 platform strains with high growth rates and/or lipid productivities. To classify the best 34 performing strains, we conducted a combined microscopic and phylogenetic analysis. 35Among the best performing strains were many coccoid green algae. Several strains 36 belong to the species Acutodesmus (Scenedesmus) obliquus and to the species Chlorella 37 sorokiniana, thus expanding on existing germplasm. Identified at the genus level were 38 some Desmodesmus strains and one Ankistrodesmus strain. Several strains were classified 39 as belonging to the genus Coelastrella, a taxon reported for the first time for North 40 America. Multiple additional strains had ambiguous identities, with some strains possibly 41 representing novel species. Reporting on the above strains, some of which have been 42tested successfully in outdoor ponds and most of which are deposited at the University of 43 Texas Culture Collection of Algae, is a step forward in expanding the biological 44 resources available for algae biofuel production.

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Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the 'host' cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host-endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the 'chassis and engine' model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.