Telonemia, a new protist phylum with affinity to chromist lineages

Abstract

Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup.

Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction

“…First, the monophyly of the clade (Rhizaria + Stramenopila) is witnessed, and the corresponding posterior probability is 100%. Compared with the corresponding value (71%) in a previous study (Shalchian-Tabrizi et al, 2006), this value is more convincing. And this clade was also supported by the evidence of expressed sequence taqs (ESTs) (Burki et al, 2007).…”

“…Due to the differences in taxa sampled and ambiguous alignment, the findings of previous phylogenetic studies based on 18S rDNAs vary extensively from each other (Cavalier-Smith and Chao, 1996;Kumar and Rzhetsky, 1996;Van de Peer and De Wachter, 1997;Burki et al, 2002;Kostka et al, 2004;Nikolaev et al, 2004;Polet et al, 2004;Shalchian-Tabrizi et al, 2006;Shalchian-Tabrizi et al, 2007). Additionally because of the effects of sparse taxon sampling and heterogeneity in the sequence data, the results of the studies based on multiple proteins or protein-coding genes are also quite different from each other (Baldauf et al, 2000;Philippe et al, 2004;Harper et al, 2005;Rodríguez-Ezpeleta et al, 2005;Burki and Pawlowski, 2006;Burki et al, 2007;Hackett et al, 2007;Patron et al, 2007;Kim and Graham, 2008).…”

Plastid Origin and Evolution: New Models Provide Insights into Old Problems

“…These taxa were hypothesized to share a single, ancient red algal secondary endosymbiosis that gave rise to the chromophyte plastid present in many photosynthetic chromalveolates such as diatoms and haptophytes and lost secondarily in groups like ciliates and the plastid-lacking cryptophyte lineage Goniomonas. Recently several other protist groups such as telonemids (Shalchian-Tabrizi et al, 2006), katablepharids, centrohelids (Okamoto and Inouye, 2005;Okamoto et al, 2009), picobiliphytes , and rappemonads (Kim et al, 2011) have been suggested to share an affiliation with the chromalveolates. Undoubtedly the quickening pace of environmental genomics research will turn up other candidate taxa affiliated with the ever-growing assemblage of chromalveolates that no longer bears any resemblance to the taxonomic scheme that was originally envisaged by Cavalier-Smith (1998).…”

Molecular biogeochemistry of modern and ancient marine microbes

“…Classification is based on Adl and colleagues (2005) and Not and colleagues (2007). All groups correspond to first and second rank according to Adl and colleagues (2005) except *Super-group and **Phylum (Shalchian-Tabrizi et al, 2006). Fig.…”