A simplified scheme of the evolution of the tetrapyrrole biosynthesis pathway with an emphasis on the models from this study (black bars).

<p>Primary endosymbiosis (PE) gave rise to the Archaeplastida comprising red algae, green algae and glaucophytes. Following the divergence of main eukaryotic lineages, secondary (SE) or tertiary endosymbiosis (TE) events equipped the ancestors of CASH taxa (cryptophytes, alveolates, stramenopiles and haptophytes) with photosynthetic capabilities. Contradictory evidence has been debated over the last years as for the history of CASH plastid acquisitions (e.g. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref005" target="_blank">5</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref008" target="_blank">8</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref034" target="_blank">34</a>]). A plastid-early scenario (the chromalveolate hypothesis) posits that all CASH taxa are monophyletic and the CASH plastid was vertically transferred (dashed red line) and lost in extant non-photosynthetic descendants (such as ciliates and most rhizarians). Plastid-late scenarios require multiple lateral acquisitions of the CASH plastid (question marks) but better reflect some current phylogenomic analyses of the plastid recipients (e.g. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref018" target="_blank">18</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref069" target="_blank">69</a>]). Loss of photosynthesis/plastids have been documented in many sister lineages, such as oomycetes or apicomplexans, however these are in line with plastid-late scenarios as well. A cryptic SE with a CASH alga or numerous HGT (red arrows) events are inferred before the divergence of extant chlorarachniophytes (this work, [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref078" target="_blank">78</a>]), which was masked by the acquisition of the current green algal endosymbiont. A similar situation in <i>L</i>. <i>chlorophorum</i> led to the peridinin plastid replacement with a green plastid, however the majority of red-related heme pathway enzymes remained functionally conserved in the successor plastid. The loss of the heterotrophic pathway possibly occurred several times independently in the stramenopile and dinoflagellate lineages, as <i>Perkinsus marinus</i>, sister to dinoflagellates, still contains a functional mitochondrial-cytosolic pathway [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166338#pone.0166338.ref008" target="_blank">8</a>].