Genomics of Preaxostyla Flagellates: Ph.D. Thesis

  • Successfully defended on January 31st 2020.



I would like to express my gratitude to my supervisor Vladimír Hampl for introducing me to the world of protistology and guiding me through this work, to my mentors Zuzana Vaitová and Anna Karnkowska for teaching me so much about laboratory work and bioinformatics, and to Andrew Roger for kindly hosting me in his laboratory in Canada.

Many thanks also to my high school biology teacher Petr Šíma for kindling my interest in the microscopic world, to my astronomy instructor Jindřiška Majorová whom I owe so much for my science soft skills, to my parents Kateřina Nováková and Vítězslav Novák for raising me in an atmosphere of curiosity and love for nature, to my partner and spouse Anna Novák Vanclová for joining me on this journey and supporting me unwaveringly, and to all my colleagues and friends for their help and care.


Protists inhabiting oxygen-depleted environments have evolved various adaptation to thrive in their niches, including modified mitochondria to various degrees adapted to anaerobiosis. The most radically altered forms of these organelles (Mitochondria-Related Organelles, MROs) have completely lost their genomes and other defining features of canonical aerobic mitochondria. Anaerobic protists are often found as endobionts (parasites, mutualists, etc.) of larger organisms. The endobiotic lifestyle combined with anaerobiosis poses another source of evolutionary pressure forcing unique adaptations in the endobionts. Here we present new insights into the adaptations of an anaerobic protistan phylum Preaxostyla, especially with regard to the reductive evolution of mitochondria, which, uniquely among all known eukaryotes, led to a complete loss of the organelle in the oxymonad Monocercomonoides exilis.

We have obtained M. exilis genomic assembly of good quality and completeness, as well as genomic and transcriptomic data of varying quality and completeness from 9 other Preaxostyla species. Based on extensive, thorough gene searches and functional gene annotation on these datasets, as well as phylogenetic analyses and protein localization experiments, we conclude: 1) M. exilis has completely lost the mitochondrion. This was likely facilitated by a replacement of the mitochondrial system for iron-sulfur (Fe-S) cluster assembly (ISC) with an unrelated SUF system of bacterial origin, which was employed for function in the cytosol; 2) Despite the loss of mitochondria, M. exilis displays no major reduction in genomic or cellular complexity compared to other anaerobic protists endowed with MROs; 3) The SUF system for Fe-S clusters assembly is present in all studied Preaxostyla and was likely gained in a single lateral gene transfer event from bacteria into a common ancestor of extant Preaxostyla. No studied member of Preaxostyla has the mitochondrial ISC system; 4) The ATP-producing arginine deiminase (ADI) pathway is present in most studied Metamonada including Preaxostyla and likely represents an ancestral feature of Metamonada. Distribution and phylogeny of the 3 ADI pathway genes among eukaryotes is consistent with presence of the pathway already in the last eukaryotic common ancestor (LECA) and their evolutionary history was shaped by frequent losses and lateral gene transfers.


Technical notes

  • Citation style: Chicago manual of style 17th edition.
  • Reference manager: Mendeley Desktop version 1.19.4.
  • Page 114 (page 14 of 14; Novák et al. BMC Evolutionary Biology. 2016. 16:197) was submitted as bitmap PDF for compliance with the PDF/A format required by the university.