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Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans.

Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E - Genome Biol Evol (2014)

Bottom Line: In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction.A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire.The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.

View Article: PubMed Central - PubMed

Affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France CNRS, UMR 6023, LMGE, Aubière, France ncorradi@uottawa.ca eric.peyretaillade@udamail.fr emmanuelle.lerat@univ-lyon1.fr.

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Phylogenetic tree of the LTR-retrotransposon class. Tree topology obtained using Bayesian analysis on the Pol proteins and rooted by the Ty1 reference element from yeast. Black circles highlight nodes with bootstrap support (BS) higher than 70% and bayesian posterior probability (BPP) values higher than 0.95, whereas red circles indicate BS higher than 50% and BPP values higher than 0.95. Absence of red and black circles indicates BPP values above 0.50. The three groups of microsporidian sequences are indicated by the red collapsed clades. For the uncollapsed version of the tree, see supplementary figure S1, Supplementary Material online. Three consensus sequences from the microsporidia Edhazardia aedis are indicated in blue. Colored frames represent the well-identified genera corresponding to Errantiviridae and Chromoviruses.
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evu178-F2: Phylogenetic tree of the LTR-retrotransposon class. Tree topology obtained using Bayesian analysis on the Pol proteins and rooted by the Ty1 reference element from yeast. Black circles highlight nodes with bootstrap support (BS) higher than 70% and bayesian posterior probability (BPP) values higher than 0.95, whereas red circles indicate BS higher than 50% and BPP values higher than 0.95. Absence of red and black circles indicates BPP values above 0.50. The three groups of microsporidian sequences are indicated by the red collapsed clades. For the uncollapsed version of the tree, see supplementary figure S1, Supplementary Material online. Three consensus sequences from the microsporidia Edhazardia aedis are indicated in blue. Colored frames represent the well-identified genera corresponding to Errantiviridae and Chromoviruses.

Mentions: The evolutionary histories of the four largest microsporidian TE superfamilies were investigated using Maximum Likelihood and Bayesian analyses of their complete consensus sequences. These confirmed that the vast majority of microsporidian LTR retrotransposons correspond to elements from the Ty3/gypsy group (fig. 2 and supplementary fig. S1, Supplementary Material online), which separate into three main groups that seem to have specifically diversified in microsporidia (i.e., they do not contain elements from other eukaryotes; see, e.g., group 1 in supplementary fig. S1, Supplementary Material online). Anncaliia algerae LTR retrotransposons displayed a pattern of extreme diversification within three main groups (39 sequences in group 3, 13 and 8 sequences in group 1 and 2, respectively). A similar pattern of diversification is also found in Ed. aedis, although the total number of sequences is much smaller than in An. algerae (28 different families; table 1). For the Merlin superfamily, microsporidian sequences clustered into eight phylogenetic groups, three of which contained 72% of all consensus sequences (fig. 3 and supplementary fig. S2, Supplementary Material online), suggesting that diversity in Merlin-like sequences in An. algerae results from several independent events of diversification within each group. The four classic groups from the Mariner/Tc1 superfamily (Mariner, Tc1, MaT, and pogo) are well supported in the phylogenetic tree (fig. 4 and supplementary fig. S3, Supplementary Material online). Nine consensus sequences of An. algerae appeared to be part of the Tc1 group along with other sequences from other microsporidia, whereas the remaining six, along with other microsporidian sequences, formed an independent group at the basis of Mariner, Tc1, and MaT groups but also independent of the pogo group. The An. algerae Tc5 consensus sequence (An. algerae Tc5 DDE1) and the one identified in No. antheraeae clustered inside the pogo group, though not together (fig. 4supplementary fig. S3, Supplementary Material online).Fig. 2.—


Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans.

Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E - Genome Biol Evol (2014)

Phylogenetic tree of the LTR-retrotransposon class. Tree topology obtained using Bayesian analysis on the Pol proteins and rooted by the Ty1 reference element from yeast. Black circles highlight nodes with bootstrap support (BS) higher than 70% and bayesian posterior probability (BPP) values higher than 0.95, whereas red circles indicate BS higher than 50% and BPP values higher than 0.95. Absence of red and black circles indicates BPP values above 0.50. The three groups of microsporidian sequences are indicated by the red collapsed clades. For the uncollapsed version of the tree, see supplementary figure S1, Supplementary Material online. Three consensus sequences from the microsporidia Edhazardia aedis are indicated in blue. Colored frames represent the well-identified genera corresponding to Errantiviridae and Chromoviruses.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4202319&req=5

evu178-F2: Phylogenetic tree of the LTR-retrotransposon class. Tree topology obtained using Bayesian analysis on the Pol proteins and rooted by the Ty1 reference element from yeast. Black circles highlight nodes with bootstrap support (BS) higher than 70% and bayesian posterior probability (BPP) values higher than 0.95, whereas red circles indicate BS higher than 50% and BPP values higher than 0.95. Absence of red and black circles indicates BPP values above 0.50. The three groups of microsporidian sequences are indicated by the red collapsed clades. For the uncollapsed version of the tree, see supplementary figure S1, Supplementary Material online. Three consensus sequences from the microsporidia Edhazardia aedis are indicated in blue. Colored frames represent the well-identified genera corresponding to Errantiviridae and Chromoviruses.
Mentions: The evolutionary histories of the four largest microsporidian TE superfamilies were investigated using Maximum Likelihood and Bayesian analyses of their complete consensus sequences. These confirmed that the vast majority of microsporidian LTR retrotransposons correspond to elements from the Ty3/gypsy group (fig. 2 and supplementary fig. S1, Supplementary Material online), which separate into three main groups that seem to have specifically diversified in microsporidia (i.e., they do not contain elements from other eukaryotes; see, e.g., group 1 in supplementary fig. S1, Supplementary Material online). Anncaliia algerae LTR retrotransposons displayed a pattern of extreme diversification within three main groups (39 sequences in group 3, 13 and 8 sequences in group 1 and 2, respectively). A similar pattern of diversification is also found in Ed. aedis, although the total number of sequences is much smaller than in An. algerae (28 different families; table 1). For the Merlin superfamily, microsporidian sequences clustered into eight phylogenetic groups, three of which contained 72% of all consensus sequences (fig. 3 and supplementary fig. S2, Supplementary Material online), suggesting that diversity in Merlin-like sequences in An. algerae results from several independent events of diversification within each group. The four classic groups from the Mariner/Tc1 superfamily (Mariner, Tc1, MaT, and pogo) are well supported in the phylogenetic tree (fig. 4 and supplementary fig. S3, Supplementary Material online). Nine consensus sequences of An. algerae appeared to be part of the Tc1 group along with other sequences from other microsporidia, whereas the remaining six, along with other microsporidian sequences, formed an independent group at the basis of Mariner, Tc1, and MaT groups but also independent of the pogo group. The An. algerae Tc5 consensus sequence (An. algerae Tc5 DDE1) and the one identified in No. antheraeae clustered inside the pogo group, though not together (fig. 4supplementary fig. S3, Supplementary Material online).Fig. 2.—

Bottom Line: In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction.A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire.The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.

View Article: PubMed Central - PubMed

Affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France CNRS, UMR 6023, LMGE, Aubière, France ncorradi@uottawa.ca eric.peyretaillade@udamail.fr emmanuelle.lerat@univ-lyon1.fr.

Show MeSH
Related in: MedlinePlus