The Phylogenetic Position of the Pelobiont Mastigamoeba balamuthi Based on Sequences of rDNA and Translation Elongation Factors EF‐1α and EF‐2

Abstract

The taxonomic position and phylogenetic relationships of the Pelobionta, an amitochondriate amoeboflagellate group, are not yet completely settled. To provide more information, we obtained sequences for the large subunit rDNA gene, the gene for translation elongation factor 1alpha, and for a large part of the gene encoding translation elongation factor 2 from a representative of this group, Mastigamoeba balamuthi (formerly Phreatamoeba balamuthi). The gene for the large subunit rDNA was unusually large compared to those of other protists, a phenomenon that had previously been observed for the gene encoding the small subunit rDNA. Phylogenetic reconstruction using a maximum likelihood method was performed with these sequences, as well as the gene encoding the small subunit rDNA. When evaluated individually, the M. balamuthi genes for the small and large subunit rDNAs and elongation factor 1alpha had a most recent common ancestor with either the Mycetozoa (slime molds) or with Entamoeba histolytica. A clade formed by M. balamuthi, E. histolytica, and Mycetozoa was not rejected statistically for any of the sequences. A combined maximum likelihood analysis using 3,935 positions from all molecules suggested that these three taxonomic units form a robust clade. We were unable to resolve the closest group to this clade using the combined analysis. These findings support the notion, which had previously been proposed primarily on cytological evidence, that both M. balamuthi and E. histolytica are closely related to the Mycetozoa and that these three together represent a major eukaryotic lineage.

Centrohelida is still searching for a phylogenetic home: Analyses of seven Raphidiophrys contractilis genes

“…cDNA was synthesized from the mRNA using Superscript III RNase HReverse Transcriptase (Invitrogen), and used for the templates for polymerase chain reactions (PCR). The primers for EF2 gene amplification were described in Arisue et al (2002). For HSP70 and HSP90 gene amplifications the following primers were used: HSP70F, 5′-RTHGGNATHGAYYTNGGNACNAC-3′ and HSP70R, 5′-TCNACYTCYTCDAYYKTNGGC-3′; HSP90F, 5′-GARACNTTYGCNTTYCARGCNGARAT-3′ and HSP90R, 5′-GCYTGNGCYTTCATDATNSDYTCCAT-3′ (R, A or G; H, A, C, or T; N, A, C, G, or T; Y, T or C; D, A, G, or T; K, G or T).…”

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba

“…The sequencing of about 1,280 ESTs of Mastigamoeba allowed us to locate confidently this species within the eukaryotic tree, something that has not been possible previously, based on the analysis of morphology (17) and a few genes (4,(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). Because this sequencing approach is not very expensive, it could be readily applied to many eukaryotic phyla for which pure culture is possible and a genome project is inconceivable (e.g., Euglena gracilis, genome size Ϸ3 ϫ 10 9 or Amoeba proteus, Ϸ3 ϫ 10 11 ).…”

“…Furthermore, Dictyostelium harbors two copies of this gene, rendering the interpretation of enolase tree problematic (E.B., unpublished work). A combined analysis of small and large subunit rDNAs and the two elongation factors (EF-1␣ and EF-2) indicates the monophyly of Conosa, but without significant statistical support, despite the use of Ϸ5,000 positions (21). In single gene analyses, Dictyostelium and Entamoeba do not generally group together (22)(23)(24)(25)(26)(27)(28).…”

Alternative Oxidase (AOX) Genes of African Trypanosomes: Phylogeny and Evolution of AOX and Plastid Terminal Oxidase Families

“…Since the relationship among these other eukaryotic lineages obtained in Tree A could not clearly be resolved, the phylogenetic position of the trypanosome AOXs could therefore not be settled conclusively. Although its resolution is unclear, the tree is very discordant with the accepted phylogeny of eukaryotes (Arisue et al 2002a, b; Arisue, Hasegawa, and Hashimoto 2005; Baldauf et al 2000; Bapteste and Philippe 2002). …”