Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Integrative and Evolutionary Biology (IEB)


Biological Sciences

First Advisor

Christopher Lane


Nephromyces, a genus in the phylum Apicomplexa, has recently been described as having a mutualistic relationship with its host: tunicates in the Molgulidae family (Saffo et al. 2010). If true, Nephromyces would be the only known example of a mutualistic apicomplexan genus. In addition to the possible switch to mutualism, Nephromyces is one of a few apicomplexan groups containing bacterial endosymbionts. To test the hypothesis that endosymbiotic bacteria facilitated the transition of Nephromyces from parasitism, the metabolic capabilities of Nephromyces and its bacterial endosymbionts need to be determined. The transition from obligate parasite to endosymbiont is predicted to involve different selective pressures leading to wide spread genomic changes. Identifying these changes will lead to a better understanding of the dynamics between the different biological players in this system.

Using data from Illumina HiSeq, we have assembled and annotated the transcriptomes of Nephromyces and Cardiosporidium cionae. Using data from a combination of platforms; Illumina MiSeq, HiSeq, and Pacific Biosciences, we have partially assembled a pan-genome for Nephromyces and have assembled the genomes of its bacterial endosymbionts. Using amplicon sequencing, we have estimated the genetic diversity and prevalence of multispecies infections of Nephromyces and its bacterial endosymbionts in its host Molgula manhattensis. In addition to the implementation of next-generation sequencing technologies, this work is also based on laboratory cultures and species isolation experiments.

With the aforementioned data we are able to describe the transcriptome of Nephromyces and Cardiosporidium as well as the genomes of all three bacterial endosymbionts, providing a basic overview of the metabolism of this system. Nephromyces and Cardiosporidium both encode a complete purine degradation pathway, which enables them to break uric acid into pyruvate and glycine, additionally Nephromyces is also able to create malate from uric acid. This could represent the primary route of carbon, nitrogen and energy acquisition in Nephromyces. The genomes of the bacterial endosymbionts are severely reduced, but relatively enriched for vitamin and amino acid biosynthesis (at least in the Betaproteobacteria and Bacteroidetes symbionts). It is likely that the bacterial endosymbionts are supplementing vitamins and amino acids to the limited diet of uric acid found in Nephromyces. Our amplicon data reveals that nearly all M. manhattensis are infected with multiple species of Nephromyces. The community of Nephromyces forms a tightly integrated system of metabolic interdependencies based of the different bacterial endosymbionts.



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.