29Recent phylogenetic analyses position certain 'orphan' protist lineages deep in the tree of 30 eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic 31 analyses that incorporate deeply sequenced transcriptomes from representatives of 32 collodictyonids (diphylleids), rigifilids, Mantamonas and ancyromonads (planomonads). 33Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel 34 supergroup-level clade that includes collodictyonids, rigifilids and Mantamonas, which we name 35 'CRuMs'. Further, they robustly place CRuMs as the closest branch to Amorphea (including 36 animals and fungi). Ancyromonads are strongly inferred to be more distantly related to 37 Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate 38 deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch 39 deeply on the lineage that includes animals, near the most commonly inferred root of the 40 eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of 41 extant eukaryotes. 42 43 Introduction 44

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

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