Collodictyon--An Ancient Lineage in the Tree of Eukaryotes

Abstract

The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the “unikont” and “bikont” groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

“…Interestingly, glaucophytes still clustered with cryptophytes in these trees [59,60] and other recently discovered related lineages, such as heterotrophic katablepharids and picozoans [61][62][63]; the latter were formerly called picobiliphytes and considered photosynthetic but available data indicate that they are heterotrophic [64,65]. Several later analyses recovered a Rhodophyta-Viridiplantae monophyly [58,62,66,67] and even a clade containing all three Archaeplastida lineages, but still mixed with cryptophytes [67], katablepharids, picozoans and the newly discovered heterotrophic flagellate Palpitomonas bilix [68]. However, the relationships were poorly supported or, at best, had moderate support.…”

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

“…Whereas phylogenomic analyses robustly recover the monophyly of Opisthokonta, Amoebozoa and SAR, the phylogenetic coherence of Excavata, Archaeplastida, and Hacrobia is less certain (see also Fig. 1) (Burki et al 2008Hampl et al 2009;Parfrey et al 2010;Brown et al 2012;Zhao et al 2012;Burki 2014).…”

“…More recently, a better understanding of protistan ultrastructural diversity and the development of phylogenomic approaches have refined this picture and further delineated these groups (see also Fig. 1) (Bapteste et al 2002;Burki et al 2007;Hampl et al 2009;Brown et al 2012;Zhao et al 2012).…”

The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae

“…Among these major lineages excavates are a putative assemblage of (often heterotrophic) flagellates, proposed on the basis of shared morphological characters (e.g., the ventral feeding groove and associated cytoskeletal structures) and molecular data. Excavates are subdivided into two subgroups, Metamonada and Discoba, the latter consistently recovered in phylogenomic analyses (Hampl et al, 2009;Zhao et al, 2012). Within Metamonada, most lineages lack typical mitochondria and instead possess hydrogenosomes (e.g., Trichomonas in parabasalids) or mitosomes (e.g., Giardia in diplomonads) (Adl et al, 2012;Walker et al, 2011).…”