Genomics of new ciliate lineages provides insight into the evolution of obligate anaerobiosis - single gene datasets for phylogenomic analysis of anaerobic ciliates (SAL, Ciliophora), protein datasets for mitochondrial pathways prediction, and mitochondrial genomes

Oxygen plays a crucial role in energetic metabolism of most eukaryotes.
Yet, adaptations to low oxygen concentrations leading to anaerobiosis have
independently arisen in many eukaryotic lineages, resulting in a broad
spectrum of reduced and modified mitochondrial organelles (MROs). In this
study, we present the discovery of two new class-level lineages of
free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and
Parablepharismea, cl. nov., that, together with the class Armophorea, form
a major clade of obligate anaerobes (APM ciliates) within the SAL
(Spirotrichea, Armophorea, Litostomatea) group. To deepen our
understanding of the evolution of anaerobiosis in ciliates, we predicted
the mitochondrial metabolism of cultured representatives from all three
classes in the APM clade, using transcriptomic and metagenomic data, and
performed phylogenomic analyses to assess their evolutionary
relationships. The predicted mitochondrial metabolism of representatives
from the APM ciliates reveals functional adaptations of metabolic pathways
that were present in their last common ancestor and likely led to the
successful colonization and diversification of the group in various anoxic
environments. Furthermore, we discuss the possible relationship of
Parablepharismea to the uncultured deep-sea class Cariacotrichea based on
single gene analyses. Like most anaerobic ciliates, all studied species of
the APM clade host symbionts, which we propose to be a significant
accelerating factor in the transitions to an obligately anaerobic
lifestyle. Our results provide an insight into the evolutionary mechanisms
of early transitions to anaerobiosis and shed light on fine-scale
adaptations in MROs over a relatively short evolutionary timeframe.