Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group

Abstract

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

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

“…In addition, a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. ). There are two sister clades in Opisthokonta, the Holozoa and the Nucletmycea (/Holomycota). They share several characters, including synthesis of extracellular chitin in an exoskeleton, cyst/spore wall or cell wall of filamentous growth and hyphae; the extracellular digestion of substrates with osmotrophic absorption of nutrients; and other cell biosynthetic and metabolic pathways.…”

“…In addition, a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. ).…”

“…Gefionella, Malawimonas . •“CRuMs” (Brown et al. ) [Varisulca Cavalier‐Smith 2012] (R)This probable sister clade in Amorphea, informally referred to as CRuMs, includes at least Collodictyonidae, Rigifilida and Mantamonas . All members exhibit some form of cellular plasticity, some with pseudopodia.Incertae sedis CRuMs: Glissandra .…”

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

“…The eukaryote tree of life is one of the oldest working hypotheses in biology. Over the past 15 years, this tree has been extensively reshaped based on transcriptomic and genomic data for an ever-increasing diversity of protists (i.e., microbial eukaryotes), and the development of more realistic models of evolution Quang et al 2008;Yabuki et al 2014;Katz 2015;Burki et al 2016;Brown et al 2018;Cavalier-Smith et al 2018;Wang et al 2018). The current picture of the tree sees most lineages placed into a few redefined 'supergroups' -a taxonomic rank-less concept that was devised as inclusive clades reasonably supported by molecular and/or morphological evidence (Simpson and Roger 2002;Simpson and Roger 2004;Keeling et al 2005).…”

A glycogenin homolog controls Toxoplasma gondii growth via glycosylation of an E3 ubiquitin ligase

“…This activity has been proposed to prime glycogen synthesis where the glycogenin sequence is found throughout fungi and metazoa. The Gat1 sequence is observed in a range of alveolates (includes T. gondii), stramenopiles (includes P. ultimum), and rhizaria (altogether known as the SAR group), and archaeplastids (with the SAR group known as bikonts), but not in the more recently emerging unikonts, that include the amoebozoa, fungi and animals (Burki, 2014;Brown et al, 2018). Since glycogenin has the complementary distribution being found only in fungi and animals, it is tempting to speculate that Gat1 is the evolutionary precursor of glycogenin.…”