EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS One 3:e2621

Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS ONE (Impact Factor: 3.23). 02/2008; 3(7):e2621. DOI: 10.1371/journal.pone.0002621
Source: PubMed


Classification of eukaryotes provides a fundamental phylogenetic framework for ecological, medical, and industrial research. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). Although the plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known.
This study was designed to test the validity of the Archaeplastida and Chromalveolata through the analysis of nucleus-encoded eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) sequences generated from the glaucophyte Cyanophora paradoxa, the cryptophytes Goniomonas truncata and Guillardia theta, the katablepharid Leucocryptos marina, the rhizarian Thaumatomonas sp. and the green alga Mesostigma viride. The HSP70 phylogeny was largely unresolved except for certain well-established groups. In contrast, EEF2 phylogeny recovered many well-established eukaryotic groups and, most interestingly, revealed a well-supported clade composed of cryptophytes, katablepharids, haptophytes, rhodophytes, and Viridiplantae (green algae and land plants). This clade is further supported by the presence of a two amino acid signature within EEF2, which appears to have arisen from amino acid replacement before the common origin of these eukaryotic groups.
Our EEF2 analysis strongly refutes the monophyly of the Archaeplastida and the Chromalveolata, adding to a growing body of evidence that limits the utility of these supergroups. In view of EEF2 phylogeny and other morphological evidence, we discuss the possibility of an alternative eukaryotic supergroup.

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    • "At some point the members of this group, which also includes the cryptophytes, haptophytes, and alveolates as well as the heterokontophytes, acquired their plastid through secondary endosymbiosis of a red alga, explained by the presence of four membranes, the outer one being continuous with the rough endoplasmic reticulum and the outer membrane of the nucleus (Keeling 2009). In recent studies of diatom genomes, however, there have been discoveries of nuclear genes of a green algal origin that are not the result of lateral gene transfer, suggesting a cryptic endosymbiont likely related to prasinophyte-like green algae in an ancestor of chromalveolates (Kim & Graham 2008). The combination of two ancient endosymbiosis events, as well as supplemental horizontal gene transfer, has provided the chromalveolates with the genetic potential to become one of "
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    ABSTRACT: Diatoms are one of the largest groups of primary producers in the oceans, yet despite their environmental importance little is known about their plastidial lipid biochemistry. It has been previously reported that Skeletonema species contain primarily C16/C16 and C20/C16 forms of mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively). Likewise, it was also reported that Phaeodactylum tricornutum contains primarily C16/ C16 and C20/C20 forms of MGDG and DGDG. We seek to relate their studies to other diatoms, both in the centrics and pennates, with particular focus on the marennineproducing pennate diatom, Haslea ostrearia. To this end, the composition and positional distribution of fatty acids of MGDG and DGDG were examined using positive-ion electrospray ionization/mass spectrometry (ESI/MS). Two centric diatoms, Skeletonema marinoi and Thalassiosira weissflogii, and the pennate diatom, P. tricornutum, contained primarily C20/C16 (sn-1/sn-2) and C18/C16 forms of MGDG and DGDG. The other pennate diatoms, H. ostrearia and Navicula perminuta, contained primarily C18/C16 or C18/C18 forms of MGDG and DGDG, indicating a previously unrecognized fatty acid diversity in diatom MGDG and DGDG.
    Phycological Research 07/2013; 61(3):199-207. DOI:10.1111/pre.12015 · 1.27 Impact Factor
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    • "We used genes for four proteins, translation elongation factor 2 (Ef-2), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), and actin. Although Ef-2 genes have proven useful in other eukaryotic lineages [20], this study represents their first use for the deep phylogeny of Fungi. Olpidium, if nested within Zygomycota, becomes a key organism for reconstructing the trail of how terrestrial fungi lost their flagella and colonized land. "
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    ABSTRACT: From a common ancestor with animals, the earliest fungi inherited flagellated zoospores for dispersal in water. Terrestrial fungi lost all flagellated stages and reproduce instead with nonmotile spores. Olpidium virulentus (= Olpidium brassicae), a unicellular fungus parasitizing vascular plant root cells, seemed anomalous. Although Olpidium produces zoospores, in previous phylogenetic studies it appeared nested among the terrestrial fungi. Its position was based mainly on ribosomal gene sequences and was not strongly supported. Our goal in this study was to use amino acid sequences from four genes to reconstruct the branching order of the early-diverging fungi with particular emphasis on the position of Olpidium. We concatenated sequences from the Ef-2, RPB1, RPB2 and actin loci for maximum likelihood and Bayesian analyses. In the resulting trees, Olpidium virulentus, O. bornovanus and non-flagellated terrestrial fungi formed a strongly supported clade. Topology tests rejected monophyly of the Olpidium species with any other clades of flagellated fungi. Placing Olpidium at the base of terrestrial fungi was also rejected. Within the terrestrial fungi, Olpidium formed a monophyletic group with the taxa traditionally classified in the phylum Zygomycota. Within Zygomycota, Mucoromycotina was robustly monophyletic. Although without bootstrap support, Monoblepharidomycetes, a small class of zoosporic fungi, diverged from the basal node in Fungi. The zoosporic phylum Blastocladiomycota appeared as the sister group to the terrestrial fungi plus Olpidium. This study provides strong support for Olpidium as the closest living flagellated relative of the terrestrial fungi. Appearing nested among hyphal fungi, Olpidium's unicellular thallus may have been derived from ancestral hyphae. Early in their evolution, terrestrial hyphal fungi may have reproduced with zoospores.
    BMC Evolutionary Biology 11/2011; 11(1):331. DOI:10.1186/1471-2148-11-331 · 3.37 Impact Factor
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    • "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). Only Opisthokonta, also known as the Fungi- Metazoa group, appears in all of the studies of eukaryote interrelationships (Parfrey et al., 2006). "
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    ABSTRACT: Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.
    Protein & Cell 02/2011; 2(2):161-70. DOI:10.1007/s13238-011-1017-2 · 3.25 Impact Factor
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