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Parasitism is a common life strategy throughout the eukaryotic tree of life. Many devastating human pathogens, including the causative agents of malaria and toxoplasmosis, have evolved from a photosynthetic ancestor. However, how an organism transitions from a photosynthetic to a parasitic life history strategy remains mostly unknown. Parasites have independently evolved dozens of times throughout the Florideophyceae (Rhodophyta), and often infect close relatives. This framework enables direct comparisons between autotrophs and parasites to investigate the early stages of parasite evolution. Parasitic red algae have traditionally been defined as either ‘adelphoparasites’, which infect hosts within their same family or tribe, or ‘alloparasites’ which infect hosts in other families. Prior to this research, investigations have primarily focused on understanding the development and evolution of ‘adelphoparasites’. All adelphoparasites studied to date have been shown to have lost their native plastid and instead incorporate a host plastid when packaging their spores. Additionally, previously published ‘adelphoparasite’ mitochondrion genomes have reduced coding capacity. The goal of this research was to investigate 1) the evolutionary impact on the plastid of the ‘alloparasite’ Choreocolax polysiphoniae, 2) the coding capacity of the C. polysiphoniae mitochondrion, and 3) the evolutionary origins of Rhodomelaceae ‘alloparasites’. A combination of Sanger-sequencing of targeted PCR products and nextgeneration sequencing of genomic DNA and total RNA was used to investigate the organelles of the ‘alloparasites’ Choreocolax polysiphoniae, Harveyella mirabilis, Leachiella pacifica, and a previously undescribed species of Leachiella, the ‘adelphoparasites’ Gracilariophila oryzoides and Gonimophyllum skottsbergii, and the host of C. polysiphoniae, Vertebrata lanosa. Organellar genomes were assembled using CLC genomics workbench and Geneious Pro and subsequently manually annotated using BLAST and Pfam. Comparative analyses of organellar genomes were completed using MAUVE genome alignment software. Total RNA was assembled using the Trinity based pipeline, Agalma and annotated using InterProScan. Analyses of transcriptomic data were completed using Silix and HiFix. This research generated plastid genomes for C. polysiphoniae and its host V. lanosa. The C. polysiphoniae plastid represents the first plastid genome sequenced for a red algal parasite. Interestingly, this plastid has reduced coding capacity and has lost genes involved with photosynthetic processes and its presence challenges the previously proposed paradigm of red algal parasite evolution. Investigations of red algal parasite mitochondria demonstrated that parasites retain fully functional and typical Florideophyceae mitochondria. Finally, an investigation of parasites typically considered as alloparasites supports a monophyletic clade of parasites, which all retain their native plastid genomes, arose and radiated to infect different hosts within the Rhodomelaceae. Data generated here supports previous findings that ‘alloparasites’ rarely infect hosts in different families. Therefore the terms ‘adelphoparasite’ and ‘alloparasite’, which are based on evolutionary relationships to their hosts and do not accurately distinguish types of red algal parasites. Based upon this research, we propose to redefine red algal parasites by their plastid origins as either Archaeplastic parasites (parasites that retain a native plastid) or Neoplastic parasites (those which incorporate a host plastid).

Organellar Genome Evolution in Red Algal Parasites: Differences in Adelpho- and Alloparasites