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Collodictyon--an ancient lineage in the tree of eukaryotes.

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K - Mol. Biol. Evol. (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Microbial Evolution Research Group, Department of Biology, University of Oslo, Oslo, Norway.

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.

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18S rDNA phylogeny of the Diphyllatia species Collodictyontriciliatum (highlighted by black box) and Diphylleia rotans. The topology was reconstructed by MrBayes v3.1.2 under the GTR + GAMMA + I + covarion model. Posterior probabilities (PP) and ML bootstrap supports (BP, inferred by RAxML v7.1.2 under GTR + GAMMA + I model) are shown at the nodes. Thick lines indicate PP > 0.90 and BP > 80%. Dashes “-” indicate PP < 0.5 or BP < 50%. A few long branches are shortened by 50% (/) or 75% (//).
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fig1: 18S rDNA phylogeny of the Diphyllatia species Collodictyontriciliatum (highlighted by black box) and Diphylleia rotans. The topology was reconstructed by MrBayes v3.1.2 under the GTR + GAMMA + I + covarion model. Posterior probabilities (PP) and ML bootstrap supports (BP, inferred by RAxML v7.1.2 under GTR + GAMMA + I model) are shown at the nodes. Thick lines indicate PP > 0.90 and BP > 80%. Dashes “-” indicate PP < 0.5 or BP < 50%. A few long branches are shortened by 50% (/) or 75% (//).

Mentions: In order to clarify the origin of Collodictyon, we first obtained the 18S rDNA sequence for C. triciliatum. Phylogenetic analysis recovered most of the eukaryote supergroups as monophyletic clades, except CCTH and Archaeplastida, congruent with several recent reports (fig. 1; Burki et al. 2007, 2008; Yoon et al. 2008; Hampl et al. 2009). More interestingly, this phylogeny robustly supported Collodictyon and Diphylleia as sister lineages with 100% bootstrap support (BP) and 1.00 posterior probabilities (PP), confirming that these two species indeed are closely related. In an attempt to enrich the species diversity for this group and estimate their potential abundance and diversity in nature, we searched for Collodictyon-like 18S rDNA sequences by blastn against the environmental database in NCBI. Twenty of the top Blast hits were used for phylogenetic analysis, but only a single partial sequence grouped with Diphylleia (results not shown), suggesting a low diversity and abundance of the Diphyllatia in the environment. This partial sequence was included in the 18S phylogeny (fig. 1).


Collodictyon--an ancient lineage in the tree of eukaryotes.

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K - Mol. Biol. Evol. (2012)

18S rDNA phylogeny of the Diphyllatia species Collodictyontriciliatum (highlighted by black box) and Diphylleia rotans. The topology was reconstructed by MrBayes v3.1.2 under the GTR + GAMMA + I + covarion model. Posterior probabilities (PP) and ML bootstrap supports (BP, inferred by RAxML v7.1.2 under GTR + GAMMA + I model) are shown at the nodes. Thick lines indicate PP > 0.90 and BP > 80%. Dashes “-” indicate PP < 0.5 or BP < 50%. A few long branches are shortened by 50% (/) or 75% (//).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351787&req=5

fig1: 18S rDNA phylogeny of the Diphyllatia species Collodictyontriciliatum (highlighted by black box) and Diphylleia rotans. The topology was reconstructed by MrBayes v3.1.2 under the GTR + GAMMA + I + covarion model. Posterior probabilities (PP) and ML bootstrap supports (BP, inferred by RAxML v7.1.2 under GTR + GAMMA + I model) are shown at the nodes. Thick lines indicate PP > 0.90 and BP > 80%. Dashes “-” indicate PP < 0.5 or BP < 50%. A few long branches are shortened by 50% (/) or 75% (//).
Mentions: In order to clarify the origin of Collodictyon, we first obtained the 18S rDNA sequence for C. triciliatum. Phylogenetic analysis recovered most of the eukaryote supergroups as monophyletic clades, except CCTH and Archaeplastida, congruent with several recent reports (fig. 1; Burki et al. 2007, 2008; Yoon et al. 2008; Hampl et al. 2009). More interestingly, this phylogeny robustly supported Collodictyon and Diphylleia as sister lineages with 100% bootstrap support (BP) and 1.00 posterior probabilities (PP), confirming that these two species indeed are closely related. In an attempt to enrich the species diversity for this group and estimate their potential abundance and diversity in nature, we searched for Collodictyon-like 18S rDNA sequences by blastn against the environmental database in NCBI. Twenty of the top Blast hits were used for phylogenetic analysis, but only a single partial sequence grouped with Diphylleia (results not shown), suggesting a low diversity and abundance of the Diphyllatia in the environment. This partial sequence was included in the 18S phylogeny (fig. 1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Microbial Evolution Research Group, Department of Biology, University of Oslo, Oslo, Norway.

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.

Show MeSH